BACKGROUND: Daily and on-demand pre-exposure prophylaxis (PrEP) has been well demonstrated to effectively prevent HIV acquisition for men who have sex with men (MSM). More than half of the MSM PrEP users in Taiwan prefer on-demand PrEP; however, on-demand PrEP involves a complicated dosing regimen because it requires precoital and postcoital dosing and sex events are hard to anticipate. Although there are a growing number of mobile apps designed to improve access to HIV prevention services and HIV medication adherence, few mobile apps focus on adherence to PrEP or are designed to accommodate a complicated, on-demand PrEP dosing schedule. OBJECTIVE: The aim of this project is to evaluate the usability of a newly developed mobile app (UPrEPU) to assist MSM PrEP users to self-monitor their adherence to either daily or on-demand PrEP using a user-centered scheme. METHODS: This research will be conducted in 2 phases: app development and usability study. In the app development phase, we will first conduct formative research with end users and stakeholders through in-depth interviews; the results will provide PrEP users' and PrEP navigators' personas as material used in the app conceptualization stage. PrEP navigators are individuals in the health care system that help HIV-negative individuals who need assistance in accessing PrEP care. A low-fidelity prototype of the app feature will be formatted by applying a participatory design approach to engage PrEP users, designers, and app developers in the design process of the app. Then, a high-fidelity prototype of the app will be developed for the usability study and refined iteratively by the multidisciplinary team and new internal testers. Internal testers include the research team consisting of experts in public health, infectious disease, and industrial design and a close network of the research team that is taking PrEP. In the usability study phase, we will enroll 70 MSM PrEP users and follow them up for 4 months. Usability, feasibility, and effectiveness of adherence monitoring will be evaluated. RESULTS: Refinement of the UPrEPU app is currently ongoing. The usability study commenced in May 2020. CONCLUSIONS: The UPrEPU app is one of the first apps designed to help MSM PrEP users to self-manage their PrEP schedule better regardless of dosing modes. With a design-thinking approach and adapting to the cultural context in Taiwan's MSM population, this novel app will have substantial potential to be acceptable and feasible and contribute to the reduction of new HIV infections. TRIAL REGISTRATION: ClinicalTrials.gov NCT04248790; https://clinicaltrials.gov/ct2/show/NCT04248790. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/20360.