Background Gay, bisexual, and other men who have sex with men continue to bear a large burden of the HIV epidemic in the United States and are among the only populations with increasing incidence in recent years. Objective The Together 5000 (T5K) Study aimed to enroll a US-based, racially diverse sample of HIV-negative men, transmen, and transwomen who are not on pre-exposure prophylaxis (PrEP) into an observational cohort to inform the design, implementation, scale-up, and evaluation of HIV prevention programs. Methods We used internet-based strategies to enroll a large, racially diverse national sample of HIV-negative men, transmen, and transwomen aged 16 to 49 years at high risk of HIV acquisition via sexual networking apps. Study participants are contacted every 6 months (in between annual surveys) for a brief survey on HIV testing, HIV diagnosis, and PrEP use (ie, attempts to access, PrEP initiation, and PrEP discontinuation). Participants complete annual self-administered at-home HIV testing and Web-based surveys. Using baseline serologic data and self-reported HIV testing history, we reconstructed a cohort of persons who were HIV negative at 12 months before baseline to estimate HIV incidence leading up to cohort enrollment. Results The study sample included 8777 participants from all 50 US states, Puerto Rico, and Guam; 50.91% (4468/8777) were persons of color and 25.30% (2221/8777) were young individuals aged 16 to 24 years. Per eligibility criteria, all T5K participants reported having sex with >2 male partners in the 90 days before enrollment, self-reported not having been diagnosed with HIV, and were not actively taking PrEP. In addition, 79.39% (6968/8777) reported >2 insertive condomless anal sex (CAS) acts, 61.02% (5356/8777) reported >1 receptive CAS acts in the past 90 days. Furthermore, most (7525/8777, 85.74%) reported never having taken PrEP. In total, 70.25% (6166/8777) were sent a self-administered at-home HIV test kit and 82.29% (5074/6166) of those sent a kit returned a sample for testing. The HIV incidence rate during the 12-month period leading up to enrollment was estimated to be 2.41 (95% CI 2.02-2.90) per 100 person-years. Conclusions A large, national, and racially diverse fully Web-based cohort of HIV-negative men, transmen, and transwomen at high risk for HIV seroconversion has successfully been recruited into longitudinal follow-up. This cohort is at high risk for HIV acquisition and can provide important insights related to the real-world uptake, impact, and equity of HIV prevention interventions in the United States. Participants can be invited to participate in trials aimed at testing strategies to improve the uptake of and engagement in these interventions. International Registered Report Identifier (IRRID) RR1-10.2196/13715