Company Overview

Investor Presentation

October 2018

Exhibit 99.1

2

Important Information

For Investor Use

The information in this presentation does not contain all of the information that a potential investor should review before investing in Aerie shares. The descriptions of Aerie

Pharmaceuticals, Inc. (the “Company” or “Aerie”) in this presentation are qualified in their entirety by reference to reports filed with the SEC. Certain information in this

presentation has been obtained from outside sources or anecdotal in nature. While such information is believed to be reliable for the purposes used herein, no representations

are made as to the accuracy or completeness thereof and we take no responsibility for such information.

Any discussion of the potential use or expected success of Rhopressa

®

(netarsudil ophthalmic solution) 0.02%, with respect to foreign approval or additional indications, and our

current or any future product candidates is subject to regulatory approval. In addition, any discussion of U.S. Food and Drug Administration (“FDA”) approval of Rhopressa

®

does

not guarantee successful commercialization of Rhopressa

®

or FDA approval of Roclatan

TM

. For more information on Rhopressa

®

, including prescribing information, refer to the full

Rhopressa

®

product label at  www.rhopressa.com.

The information in this presentation is current only as of its date and may have changed or may change in the future. We undertake no obligation to update this information in

light of new information, future events or otherwise. We are not making any representation or warranty that the information in this presentation is accurate or complete.

Certain statements in this presentation, including any guidance or timelines presented herein, are “forward-looking statements” within the meaning of the federal securities

laws. Words such as “may,” “will,” “should,” “would,” “could,” “believe,” “expects,” “anticipates,” “plans,” “intends,” “estimates,” “targets,” “projects,” “potential” or similar

expressions are intended to identify these forward-looking statements. These statements are based on the Company’s current plans and expectations. Known and unknown

risks, uncertainties and other factors could cause actual results to differ materially from those contemplated by the statements. In evaluating these statements, you should

specifically consider various factors that may cause our actual results to differ materially from any forward-looking statements. In particular, FDA approval of Rhopressa

®

does

not constitute approval of Roclatan™, and there can be no assurance that we will receive FDA approval for Roclatan™ or any future product candidates. Any top line data

presented herein is preliminary and based solely on information available to us as of the date of this presentation and additional information about the results may be disclosed

at any time. In particular, FDA approval of Rhopressa

®

does not constitute FDA approval of Roclatan™, and there can be no assurance that we will receive FDA approval for

Roclatan™ or any future product candidates. FDA approval of Rhopressa

®

also does not constitute regulatory approval of Rhopressa

®

in jurisdictions outside the United States

and there can be no assurance that we will receive regulatory approval for Rhopressa

®

in jurisdictions outside the United States. Our receipt of a Prescription Drug User Fee Act

(“PDUFA”) goal date notification for Roclatan™ does not constitute FDA approval of the Roclatan™ New Drug Application (“NDA”), and there can be no assurance that the FDA

will complete its review by the PDUFA goal date of March 14, 2019, that the FDA will not require changes or additional data that must be made or received before it will approve

the NDA, if ever, or that the FDA will approve the NDA.  In addition, the preclinical research discussed in this presentation including, without limitation, the development efforts

stemming from Aerie’s collaboration with DSM for the treatment of age-related macular degeneration or other ophthalmic uses, is preliminary and the outcome of such

preclinical studies may not be predictive of the outcome of later trials. Any future clinical trial results may not demonstrate safety and efficacy sufficient to obtain regulatory

approval related to the preclinical research findings discussed in this presentation. These risks and uncertainties are described more fully in the quarterly and annual reports

that we file with the SEC, particularly in the sections titled “Risk Factors” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations.” Such

forward-looking statements only speak as of the date they are made. We undertake no obligation to publicly update or revise any forward-looking statements, whether because

of new information, future events or otherwise, except as otherwise required by law.

3

Aerie IOP–Reducing Products (IP 2030+)

Pipeline Activities

•

Rhopressa

®

–

24-hour IOP reduction, normal tension glaucoma, etc.

•

Retina

Program

–

AR-13503

and

AR-1105

implants

•

Sustained Release / Implant Manufacturing Platform

•

Beyond

Ophthalmology

–

potential

for

Aerie-owned

molecules

•

Rhopressa

®

(netarsudil ophthalmic solution) 0.02%

•

Successfully launched in U.S. April 30, 2018

•

Roclatan™ (netarsudil / latanoprost ophthalmic solution) 0.02% / 0.005%

•

U.S. NDA accepted, PDUFA set for March 14, 2019

Aerie Overview

Data on file

For Investor Use

•

Globalization

Plan

Under

Way

–

Europe

and

Japan

Rhopressa

®

: Market Perspective

Refer

to

the

full

Rhopressa

®

product

label

at

www.rhopressa.com

For Investor Use

-

~$3B Market, 37M TRx, 61M bottles

-

Half of volume first-line (PGAs)

-

Half of volume 2-3X/Day Adjuncts

-

New drug class per drug databases

-

Once-daily

dosing

directed

at

site

of

pathology,

the

trabecular

meshwork

-

Consistent

IOP

reduction

over

12

months

and

across

all

IOPs

tested,

as  

demonstrated in clinical trials     

2017 U.S. Glaucoma Market

Rhopressa

®

: HCP’s Positioning as Concomitant Therapy

Graph

Source:

IQVIA

TRx

Data

CAI: Carbonic Anhydrase Inhibitor

AA: Alpha Agonist

BB: Beta Blocker

Lumigan

8%

Travatan

7%

Latanoprost

37%

BB 13%

Fixed

Combo

15%

AA

10%

CAI

10%

4

5

5

Rhopressa

®

Formulary Coverage Increasing

For Investor Use

25%

40%

12%

40%

55%

45%

Preferred Tier

Non-preferred Tier

As of 10/01/18:

~85% of Commercial Lives Covered

~40% Medicare Part D Lives Covered

------------Commercial-------------

-----------Medicare Part D---------

9/01/18                    10/01/18                    9/01/18                  10/01/18

6

Rhopressa

®

U.S. Launch Update

Weekly IQVIA Total Rx’s and Extended Units:

For Investor Use

Week 24: 9/21/18

*Holiday Weeks

**Actual

bottles

dispensed

exceed

TRx’s

due

to

extended

supply

plans

(e.g.,

90

days’

supply)

Rhopressa

®

has not been approved by any regulatory authority other than the FDA.

Week Ending 9/30/18:

Wholesaler Shipments

to Pharmacies = 5,876

7

7

Early

Rhopressa

®

Feedback

Physician Examples:

End-stage glaucoma patient at brink of needing surgery. Patient on

maximal medical therapy (PGA/Combo/CAI) with IOP of 18 mmHg.

Added Rhopressa

®

and IOP dropped to 13 mmHg, avoiding surgery.

Patient on maximal drug therapy and inadequately controlled at 16

mmHg, with patient requiring surgery as next step. Patient IOP reduced

to 12 mmHg with Rhopressa

®

and surgery canceled.

Physician added Rhopressa

®

to a patient on two medications, and

Rhopressa

®

reduced IOP from 42 mmHg to 9 mmHg.

Patient on first-line and adjunct, physician replaced previous adjunct with

Rhopressa

®

and reduced IOP from 24 mmHg to 15 mmHg.

For Investor Use

Observations on file are anecdotal, do not reflect the results of clinical trials, and are not necessarily

indicative of the entire population

8

Active Engagement at Key Conferences

American Glaucoma

Society (AGS)

March 2018

American Society of

Cataract and Refractive

Surgeons (ASCRS)                  

April 2018

Association of

Research in Vision

and Ophthalmology

(ARVO)              

April 2018

European Glaucoma

Society (EGS)

Florence, May 2018

&

European Society of

Cataract and Refractive

Surgeons

(ESCRS)

Vienna, September

2018

For Investor Use

Roclatan

TM

(netarsudil / latanoprost ophthalmic solution) 0.02% / 0.005%

Positioning as First Line Therapy:

•

Benefits

of

Rhopressa

®

while

also

targeting

the

secondary

drain

•

Achieved statistical superiority to market-leading latanoprost

-

At each of nine time points in each of the two Phase 3 trials

•

We

believe

it

may

have

the

potential

to

become

the

most

efficacious

IOP-reducing

medication

for

glaucoma

or

ocular

hypertension,

if

approved

Roclatan

TM

Combination

Product

Candidate

For Investor Use

PDUFA Date Set for March 14, 2019

9

Data

on

file

Roclatan™

has

not

been

approved

by

the

FDA

10

Roclatan

Efficacy and Safety

Efficacy:

•

Roclatan

demonstrated statistical superiority over its components (market-

leading PGA latanoprost and Rhopressa

®

) in Mercury 1 and 2 Phase 3 trials, at

all measured time points

•

Consistent incremental IOP-reduction over latanoprost and Rhopressa

®

in the

range of 1 to 3 mmHg

Safety:

•

No treatment-related serious adverse events and minimal evidence of

treatment-related systemic effects. The most common adverse event is

conjunctival hyperemia with ~60% incidence, majority mild and sporadic and

present in 20% of subjects at baseline

•

Other ocular AEs occurring in ~5-15% of subjects receiving Roclatan

included: cornea verticillata, conjunctival hemorrhage, eye pruritus, lacrimation

increased, visual acuity reduced, blepharitis and punctate keratitis 

Data on file                                                                                                                  

For Investor Use

TM

TM

TM

11

Roclatan

Phase 3 Month 12 Responder Analysis:

Goal is to Achieve Lowest IOP Possible

At Month 12:  % of Patients

with IOP Reduced to 18 mmHg or Lower

*p<0.05, **p<0.01, ***p<0.0001

++

Data on File

Based on Mercury 1 Interim Analysis 2

For Investor Use

TM

12

Roclatan™ Next Steps

•

Roclatan

NDA submission accepted, with March 14, 2019

PDUFA

•

Current U.S. sales force will be trained on Roclatan

in  

advance of PDUFA

•

Commercial formulary access expected to be finalized

post-approval

•

Medicare Part D formulary submission to payers expected

in April 2019

For Investor Use

TM

TM

13

Expanding Aerie Franchise: Europe and Japan

•

Europe (2017 Europe “Big 5” Glaucoma Market: 91M units per year, 1.5X U.S.

units)

•

Expect to file MAA for Rhopressa

®

in 2018

•

Current clinical plan expected to satisfy European regulatory requirements

(including Rocket 4 for Rhopressa

®

and Mercury 3 for Roclatan

)

•

Mercury 3: 6-month safety and 90-day efficacy registration trial comparing

Roclatan

for non-inferiority to a fixed-dose combo in Europe (Ganfort

®

)

•

Construction of Ireland Plant in process to support worldwide commercial

supply

•

Japan (2017 Glaucoma Market: 54M units per year)

•

Advancing clinical development on our own, establishing branch office in Tokyo

•

Phase 1 completed and Phase 2 under way in the U.S. on Japanese and

Japanese-Americans; additional Phase 2 to commence in Japan

•

Phase 3 trials expected to be conducted in Japan

For Investor Use

TM

TM

Europe Glaucoma Market:

Aerie Expects to Commercialize on Its Own (if approved)

“Big

5”

Europe

Glaucoma

Market

–

2017

$1.0B; 91M TRx*, Market Share in TRx

PGA: Prostaglandin Analogue; BB: Beta Blocker; AA: Alpha Agonist; CAI: Carbonic Anhydrase Inhibitor

Sources:

IQVIA

Analytics

Link

at

ex-manufacturer

price

level.

*TRx

calculated

from

IQVIA

unit

data

(1

month

=

1

TRx)

Non-PGA Market (47%)

PGA Market (53%)

Bimatoprost

Travoprost

Latanoprost

Tafluprost

1%

PGA Fixed

Combo

BB

Non-PGA

Fixed Combo

AA

CAI

17%

11%

13%

4%

19%

10%

5%

2 -

4 Times Daily

Once Daily

17%

Others

2%

For Investor Use

14

Japan Glaucoma Market:

Aerie Expects to Partner for Commercialization (if approved)

PGA: Prostaglandin Analogue; BB: Beta Blocker; AA: Alpha Agonist; CAI: Carbonic Anhydrase Inhibitor

Sources:

IQVIA

Analytics

Link

at

ex-manufacturer

price

level.

*TRx

calculated

from

IQVIA

unit

data

(1

month

=

1

TRx)

Non-PGA Market (48%)

PGA Market (52%)

Unoprostone

Bimatoprost

Travoprost

Latanoprost

Tafluprost

PGA Fixed

Combo

BB

Non-PGA

Fixed Combo

AA

CAI

ROCK

Inhibitors

Others

13%

9%

9%

12%

19%

6%

5%

2 -

4 Times Daily

Once Daily

(Unoprostone

is bid)

11%

Japan

Glaucoma

Market

–

2017

$0.8B; 54M TRx*, Market Share in TRx

8%

4%

2%

For Investor Use

15

16

Advancing the Pipeline

AR-13503 and AR-1105 are preclinical stage molecules and have not been approved by the FDA

Additional

potential

Rhopressa

®

indications

are

being

considered

for

further

study

and

are

not

labeled

indications.

•

Rhopressa

®

Research Targets

•

24-hour IOP reduction

•

Potential in normal tension glaucoma

•

Aqueous

humor

dynamics

(trabecular

outflow,

episcleral

venous

pressure)

•

Pseudoexfoliative

glaucoma

•

Corneal healing

•

Retina Program Opportunities:

AR-1105 (dexamethasone steroid) potentially for DME

AR-13503 (ROCK/PKC inhibitor) potentially for AMD and DME

•

Drug Delivery Platform

•

Focused on ophthalmic sustained release                         

technologies

(DSM

/

PRINT

®

)

For Investor Use

17

17

Retinal Eye Diseases –

Aerie’s Next Chapter

The retinal disease market is twice that of glaucoma with $4.9 billion in

the U.S. and $9 billion worldwide per IQVIA

Current treatments lose efficacy over time, some have very serious

side effects and there are limited surgical options

The majority of current treatments require repeated injections into the

patient’s eye

Aerie has two preclinical molecules for the treatment of retinal disease:

-

AR-1105 (dexamethasone steroid) for DME

-

AR-13503 (ROCK/PKC Inhibitor) for AMD/DME

Aerie also has implant and associated manufacturing platform

technologies

For Investor Use

AR-1105 and AR-13503 are preclinical stage molecules and have not been approved by the FDA

18

18

2017 U.S. Retinal Disease Market

For Investor Use

2017 Sales: $5.3B

Unit Sales: 6.8M

Sources: Mix of public information, IQVIA and estimates         

Eylea,

$3.70

Avastin,

$0.02

Lucentis,

$1.44

steroids,

$0.15

others,

$0.02

Eylea,

2.61

Avastin,

3.03

Lucentis,

0.86

steroids,

0.23

others,

0.11

19

19

AR-1105: Dexamethasone Implant

•

Target indications

•

Macular edema due to diabetic retinopathy (DME)

•

Macular edema due to retinal vein occlusion (RVO)

•

Unmet need

•

First line anti-VEGF agents often not sufficient even with monthly intravitreal

(IVT) injections

•

Current second-line steroid treatments have limitations due to side effects

and/or injection frequency

For Investor Use

Data on File

AR-1105 may have the potential to lower treatment burden

and improve outcomes

•

2x sustained efficacy: injections every 6 months vs. every 3 months

•

Safety: Better control of drug elution, lower exposure of non-target

tissues

•

Improved IVT delivery: applicator has smaller needle (25G)

AR-1105 is a preclinical stage molecule and has not been approved by the FDA

20

AR-13503: A First-in-Class ROCK/PKC Inhibitor for the

Treatment of Wet AMD and DME

•

Active metabolite of netarsudil

•

Potential to improve outcomes by targeting multiple

disease processes

•

Monotherapy shows strong efficacy in preclinical models

•

Effective as adjunct to anti-VEGF therapy in preclinical

models

•

Expect durable treatment effect with injection frequency

of

once

every

4

–

6

months

For Investor Use

AR-13503 is a preclinical stage molecule and has not been approved by the FDA

21

Oxygen-induced retinopathy (OIR) mouse model -

PDR

Administration: Intraperitoneal QD

For Investor Use

Preclinical

AR-13503

Provides

Efficacy

Similar

to

Eylea

®

in a Proliferative Diabetic Retinopathy Model

Vehicle

(n=14)

1.25 mg/kg AR-13503

(n=16)

1 mg/kg Eylea

(n=14)

Data on File

For

more

information

on

Eylea®

please

see

the

product

webpage

https://www.eylea.us/

21

22

AR-13503

Synergistic

to

Eylea

®

in

Mouse

Model

of

Proliferative Diabetic Retinopathy

Oxygen-induced

retinopathy

(OIR)

mouse

model

-

PDR

0%

5%

10%

15%

20%

25%

30%

35%

Vehicle

n=12

Eylea (sub-

optimal dose)

n=12

AR-13503 (sub-

optimal dose)

n=14

Combination

n=8

-40%

***

*

Administration: Intraperitoneal QD

* :    p<0.01

*** : p<0.0001

For Investor Use

-60%

Data on File

Sub-optimal dose levels selected in the study to provide less than maximal efficacy

For

more

information

on

Eylea®

please

see

the

product

webpage

https://www.eylea.us/

Neovascular Area (+SEM)

23

DSM

Collaboration

–

Implant

Delivery

Technology

•

Bio-erodible implant technology

•

Aerie now has a worldwide exclusive license for all ophthalmic indications

•

Broad sustained release platform for treatment of Wet AMD and DME, as well

as glaucoma

•

Promising results from ongoing feasibility study

•

Evaluating AR-13503 (ROCK/PKC inhibitor) and related Aerie compounds

•

Linear sustained elution rates over several months

•

Achieved target retinal drug concentrations

•

Aerie also has access to DSM’s preclinical stage latanoprost implant for

glaucoma

For Investor Use

Data on File

24

PRINT

®

Technology for Ophthalmology

Micropatterned

Template

Mold formation

Mold Filling

(e.g. drug/polymer)

Particle Array

PRINT= Particle Replication In Non-wetting Templates

Aerie has the rights to use this technology for ophthalmic applications

Proprietary technology capable of creating precisely engineered sustained-release

products using fully scalable manufacturing processes

Expected to accelerate development of Aerie’s retinal disease program, including

pre-clinical AR-13503 and AR-1105, and other ophthalmic indications

For Investor Use

Excellent Control Over Particle Size, Shape and Formulation:

Aerie’s Ophthalmic Implant Manufacturing Platform

25

Evaluating Aerie’s 3,500+ Owned Molecules

•

Commencing screening for

additional indications beyond

ophthalmology

•

ROCK inhibition should have

potential in:

•

Pulmonary health,

including pulmonary

fibrosis and bronchial

asthma

•

Dermatology indications

•

Cancer

•

Others

Relationship tree of human kinases.  TK, TKL, STE, CK1, AGC, CAMK, CMGC, Other: Kinase superfamilies

For Investor Use

Aerie molecules inhibit

both ROCK1

and ROCK2

ROCK

26

Summary

•

Key Priorities

•

Rhopressa

®

:  Successful launch execution

•

Roclatan

:   U.S. PDUFA set for March 14, 2019                                                              

•

Globalization Strategy

•

Europe/Japan clinical path and commercialization strategy

•

Ireland Manufacturing Facility

•

Research Initiatives

•

Rhopressa

®

24-hour IOP reduction, normal tension glaucoma,

aqueous humor dynamics, pseudoexfoliative

glaucoma, corneal healing    

•

Retina Program:

-

File IND for AR-1105 in 4Q 2018 and AR-13503 in 1H 2019, enter clinic in 2019

•

Broad sustained release ophthalmic implant and manufacturing platform

•

Evaluating Aerie’s ROCK inhibitors beyond ophthalmology

•

Well-Financed

•

$286M cash/investments at 6/30/18; $100M undrawn credit facility

For Investor Use

TM