BACKGROUND: Widespread smartphone use provides opportunities for mobile health HIV prevention strategies among at-risk populations. OBJECTIVE: This study aims to investigate engagement in a theory-based (information-motivation-behavioral skills model) mobile phone app developed to support HIV pre-exposure prophylaxis (PrEP) adherence among Thai young men who have sex with men (YMSM) and young transgender women (YTGW) in Bangkok, Thailand. METHODS: A randomized controlled trial was conducted among HIV-negative YMSM and YTGW aged 15-19 years initiating daily oral PrEP. Participants were randomized to receive either youth-friendly PrEP services (YFS) for 6 months, including monthly contact with site staff (clinic visits or telephone follow-up) and staff consultation access, or YFS plus use of a PrEP adherence support app (YFS+APP). The target population focus group discussion findings and the information-motivation-behavioral skills model informed app development. App features were based on the 3Rs-risk assessment of self-HIV acquisition risk, reminders to take PrEP, and rewards as redeemable points. Dried blood spots quantifying of tenofovir diphosphate were collected at months 3 and 6 to assess PrEP adherence. Tenofovir diphosphate ≥350-699 fmol/punch was classified as fair adherence and ≥700 fmol/punch as good adherence. Data analysis on app use paradata and exit interviews were conducted on the YFS+APP arm after 6 months of follow-up. RESULTS: Between March 2018 and June 2019, 200 participants with a median age of 18 (IQR 17-19) years were enrolled. Overall, 74% (148/200) were YMSM; 87% (87/100) of participants who received YFS+APP logged in to the app and performed weekly HIV acquisition risk assessments (log-in and risk assessment [LRA]). The median duration between the first and last log-in was 3.5 (IQR 1.6-5.6) months, with a median frequency of 6 LRAs (IQR 2-10). Moreover, 22% (22/100) of the participants in the YFS+APP arm were frequent users (LRA≥10) during the 6-month follow-up period. YMSM were 9.3 (95% CI 1.2-74.3) times more likely to be frequent app users than YTGW (P=.04). Frequent app users had higher proportions (12%-16%) of PrEP adherence at both months 3 and 6 compared with infrequent users (LRA<10) and the YFS arm, although this did not reach statistical significance. Of the 100 participants in the YFS+APP arm, 23 (23%) were interviewed. The risk assessment function is perceived as the most useful app feature. Further aesthetic adaptations and a more comprehensive rewards system were suggested by the interviewees. CONCLUSIONS: Higher rates of PrEP adherence among frequent app users were observed; however, this was not statistically significant. A short app use duration of 3 months suggests that they may be useful in establishing habits in taking daily PrEP, but not long-term adherence. Further studies on the specific mechanisms of mobile phone apps that influence health behaviors are needed. TRIAL REGISTRATION: ClinicalTrials.gov NCT03778892; https://clinicaltrials.gov/ct2/show/NCT03778892.