Copyright © 2018. Cue Biopharma Corporate Overview Nasdaq: CUE May 17th, 2018 Exhibit 99

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Cue Biopharma Investment Highlights Scalable business for rapidly generating a pipeline of precision, injectable biologics for selectively modulating T cells Immuno-STAT™ (Selective Targeting and Alteration of T cells) Platform: A modular protein engineering solution to immunotherapy Planned IND submission for lead immuno-oncology asset (CUE-101) in Q1 2019 Autoimmune partnership with Merck Ex vivo translational biology can lower clinical risk and increase speed to approval Potential for strategic partnering transactions Multiple significant value creating opportunities over next 18 months A next-generation immunotherapy company addressing oncology and autoimmune diseases

T Cells are Fundamental to a Healthy and Functional Immune System T cells are key for providing protective immunity against pathogens and tumors (beneficial for the host) or for driving self-reactive responses in autoimmune diseases (detrimental to the host) Antigen-presenting cells (APCs) display proteins called peptide major histocompatability complexes (pMHCs) T cells recognize pMHCs through a specialized cell surface receptor, the T cell receptor (TCR) APCs deliver signals to modulate T cell activity: Co-stimulatory for expansion to respond to threats Inhibitory to protect from attacks against self T cells interact directly with APCs to modulate diverse immune responses T Cell T Cell T Cell T Cell T Cell T Cell T Cell T Cell X Antigen-Presenting Cell (APC) Co-stimulatory Signal Peptide MHC Inhibitory Signal Peptide MHC T Cell Receptor (TCR) Activating Receptor Inhibiting Receptor

Selectively Modulating Disease-Associated T Cells Immuno-STATs™ direct the potency of co-stimulatory ligands to antigen-specific T cell populations Fc Immuno-STAT™ Framework MHC - peptide (TCR Targeting) Co-stimulatory ligand(s) (Activating/Inhibitory Signal) IgG1 Fc Domain (Stability/Manufacturability) Co-Stimulatory Ligands

T cell Modulation by Leveraging Specificity of T cell Receptors Immuno-STATs™ target TCRs on disease-associated T cells through their natural specific ligands: peptide-MHC (pMHC) Once the target TCR is bound, Immuno-STATs™ safely deliver potent immune activators to the T cell Activating signals stimulate T cells to proliferate, expand, and acquire effector function to kill cancer cells: IO-STAT™ Inhibitory signals selectively ablate or downmodulate autoreactive T cells in autoimmune diseases: AI-STAT™ Immuno-STATs™ bind to disease-associated T cells to modulate immune responses T Cell T Cell T Cell T Cell T Cell T Cell T Cell X T Cell IO-STAT™ AI-STAT™ Activating Ligand (e.g., IL-2) Inhibitory Ligand (e.g., PD-L1)

Targeted Delivery of IL-2 to Disease Associated T Cells Interleukin-2 (IL-2) is a highly-potent, well-validated T cell activator shown to synergize with anti-PD-1 IL-2 domain of CUE-100 has been modified to bias binding to the CD8+ T cells of interest Allowing the pMHC to guide binding: broad therapeutic window potential Reducing binding to CD4+ Tregs: higher efficacy potential Pre-clinical data supports targeting IL-2 to disease-associated T cell subsets enhances efficacy and significantly reduces dose-limiting toxicities Represents a potential breakthrough for selective delivery of IL-2 to disease relevant T cells Fc CUE-100 Framework 2x vIL-2 pMHC

CUE-101 is Exemplary Approach in Oncology Rationale E7 protein is a tumor-specific driver of oncogenesis Highly immunogenic epitope HPV+ cancers affect ~25,000 Americans annually Extensive clinical characterization of IL-2 and Clinical data from ACT (Adoptive Cellular Therapy) targeting same T cell population with significant clinical benefit1 CUE-101 delivers IL-2 to direct T cells against HPV+ cancers Fc T cell targeting: HLA-A*-0201 / HPV E7 pMHC Co-stimulatory Signal: 2x IL-2 variant 1Stevanovic, S., et. al. Complete regression of metastatic cervical cancer after treatment with human papillomavirus-targeted tumor-infiltrating T cells. J Clin Oncol. 2015 May 10;33(14):1543-50.

Validating Immuno-STATs™ Through Human Ex Vivo Assays A highly-efficient translational approach to drug discovery + Extract Blood from Patients Isolate T cells Add IO-STAT™ to T cells Assay Selective Activation and Expansion Drug candidates are screened against human blood samples for selective activation (or ablation) of disease associated T cells We believe the ability to rapidly assay activity of drug constructs on human T cells has potential to decrease costs, increase productivity and provide greater insights for clinical trial design

Expansion: CUE-101 Expands Human HPV-Specific T Cells from Blood Samples CUE-101 expands HPV reactive CD 8+ T cells from HPV+ donor Day 0 Day 17 Pre Stim CUE-101, 100nM 0.002% CD8+ T cells Antigen Specific T cells (HPV-E711-20 Tetramer) 0.086% Day 0 CUE-101 Stimulation Day 9 CUE-101 Re-stimulation Day 17 Analysis Stimulation Schedule Results > 40X increase

Engagement: Targeting IL-2 to Specific T cells Supports an Attractive Therapeutic Window Monitoring pSTAT5 on human PBMC supports >100 fold EC50 window HPV E711-20 CD8+ (EC50 = 2.8 nM) Bulk PBMC CUE-101 Off-target binding does not appear to emerge until very high doses: well beyond the dose range of target T cells being activated Target T cell activation and proliferation

CUE-101 Activates Target T Cells into Cytotoxic “Killer” T Cells CUE-101 treated HPV reactive human T cells show markers for cell killing ability CUE dose CUE-101 CUE-100 (CMV) 1.0 nM 3.2 nM 10.0 nM 31.7 nM 100 nM Media only PMA/iono 0.3 nM IFNg TNFa GrzB CUE-101 (HPV) (EC50 = 6.0 nM) CUE-100 (CMV) No. Spot Forming Cells [CUE Biologic] nM IFNg/TNFα/GrzB = “Killer T cells”

Anti-tumor Efficacy in HPV-driven TC-1 Tumor Model with mCUE-101 Correlates with Increases in Target T cell Population Target T cell Population Vehicle mCUE-101 αPD-1 Combination 0/10 0/10 2/10 7/10

Previously Treated Mice Resist Tumor Re-challenge: Demonstrates Immunological Memory Complete responders re-challenged after two months: no additional therapy given

Using Patient Samples to Select and Stratify Patients Potentially Provides a Translational Approach to Clinical Trials + Extract Blood from Patients Isolate T cells Add IO-STAT™ to T cells Assay Selective Activation and Expansion Patient samples may be tested prior to treatment to select and stratify patient enrollment We believe the ability to rapidly assay activity of drug constructs on human T cells has potential to decrease costs, increase productivity and provide greater insights for clinical trial design

Ex Vivo Translational Studies Support Precision Medicine-Based Clinical Development CONFIDENTIAL & PROPRIETARY Leveraging Ex Vivo translational biology may lower clinical risk and increase speed to approval Phase I Phase II Phase III Phase I Phase II Ex Vivo Translational Dose Escalation Toxicity/Safety Statistical Analysis Refine Dose Survey Efficacy Pivotal Efficacy Comparison to Standard Registration Registration Define Dose Range Predictive Biomarkers Patient Stratification Refine Dose Toxicity/Safety Survey Efficacy Pivotal Efficacy Comparison to Standard Traditional Development Translational Development Phase I(b) Expanded Survey

Expanding the CUE-100 Series to New Indications A simple peptide swap enables previously-validated framework to target new indications Different antigens on validated framework create new drugs Rapidly validates additional disease indications and pipeline Leveraging ex vivo assays to identify epitopes for oncology portfolio expansion CUE-101 HLA A:02, IL-2, HPV-E7 CUE-102 HLA A:02, IL-2, TBD CUE-103 HLA A:02, IL-2, TBD CUE-100 Framework Peptide Epitopes +

Immuno-STAT™ Platform for Targeting Autoimmune Diseases Developing biologics to selectively ablate or inhibit disease-associated T cells Fc CUE MHC Class I Soluble pMHC I /II (CTL TCR Targeting) Co-Inhibitory/Regulatory CUE MHC Class II Directly depletes disease-associated cytolytic T cells (CTLs) recognizing self antigens can create focused holes in the immune system Inhibits disease-associated T cells via direct targeting of CD4 cells and generation of T-regulatory cells (Tregs)

Financial Summary and Capital Structure Initial Public Offering completed December 27, 2017 Issued 8,820,710 shares at a $7.50 Received approximately $62 million in net proceeds As of March 31, 2018: $280 million in market capitalization 20,130,766 common stock shares outstanding $53.1 million in cash Positive financial position to further development of the Immuno-STATTM Biologics platform and begin clinical studies

Potential Value Creating Activities for 2018-2019 Planned submission of IND for CUE-101 in Q1 2019 Continue development of pipeline Nomination of new CUE-100 Series assets CUE-102/103 Ongoing data from human clinical samples in ex vivo assays Further development and refinement of ex vivo assay capabilities to support pipeline and clinical development Achieve proof of mechanism/concept in Merck autoimmune program

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