Background People living with HIV (PLWH) presenting with advanced HIV have worse outcomes than those diagnosed earlier. The proportion of PLWH in Indonesia who are late presenters is unknown but likely high. Identifying factors associated with late presentation is key to earlier diagnosis and intervention. Methods Adult PLWH were enrolled at 19 centers across Indonesia (2018–2020) in the INA-PROACTIVE observational cohort study. Late presentation was defined as having a CD4+ count <350 cells/μl within 3 months of diagnosis. Risk factors were assessed using multivariable logistic regression. Findings Among 3201 eligible participants, 2790 (87·2%) were late presenters. High proportion of late presenters was observed from 2015 to 2019 (83·3%–89·8%). Characteristics associated with late presentation included age 30–39 (aOR = 1·47, 95% CI: 1·15–1·90) or age ≥40 (aOR = 1·71, 95% CI: 1·21–2·46) vs. age 18–29; male sex (aOR = 2·93, 95% CI: 2·07–4·24); diagnosis in ≤2015 (aOR = 1·45, 95% CI: 1·12–1·89); and diagnosis through Provider-Initiated Testing and Counseling (aOR = 2·38, 95% CI: 1·86–3·04) vs. Voluntary Counseling and Testing (VCT). Suspected MSM transmission was associated with lower odds of late presentation (aOR = 0·57, 95% CI: 0·39–0·82) compared to heterosexual transmission. Interpretation Late presentation remains highly prevalent in Indonesia. Expanded efforts are needed to promote testing among those at risk. Targeted interventions for older adults, men, and non-MSM populations, alongside VCT and MSM-focused programs, may help reduce late HIV diagnosis and improve early management. Funding This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health , under contract No. 75N91019D00024 Task orders 75N91020F00004, 75N91020F000012. © 2026 The Author(s).