Little is known about the prevalence of and factors that influence retention in HIV-related care among Indonesian men who have sex with men (MSM) and transgender women (transwomen, or waria in Indonesian term). Therefore, we explored the driving factors of retention in care among HIV-positive MSM and waria in Indonesia. This cross-sectional study involved 298 self-reported HIV-positive MSM (n = 165) and waria (n = 133). Participants were recruited using targeted sampling and interviewed using a structured questionnaire. We applied a four-step model building process using multivariable logistic regression to examine how sociodemographic, predisposing, enabling, and reinforcing factors were associated with retention in care. Overall, 78.5% of participants were linked to HIV care within 3 months after diagnosis or earlier, and 66.4% were adequately retained in care (at least one health care visit every three months once a person is diagnosed with HIV). Being on antiretroviral therapy (adjusted odds ratio [AOR] = 6.00; 95% confidence interval [CI]: 2.93-12.3), using the Internet to find HIV-related information (AOR = 2.15; 95% CI: 1.00-4.59), and having medical insurance (AOR = 2.84; 95% CI: 1.27-6.34) were associated with adequate retention in care. Involvement with an HIV-related organization was associated negatively with retention in care (AOR = 0.47; 95% CI: 0.24-0.95). Future interventions should increase health insurance coverage and utilize the Internet to help MSM and waria to remain in HIV-related care, thereby assisting them in achieving viral suppression.