Background In 2013, the Indonesian government launched the strategic use of antiretroviral therapy (SUFA) initiative with an aim to move closer to achieving the UNAIDS 90-90-90 target. This study assessed the impact of SUFA on the cascade of HIV care. Methods We performed a two-year retrospective population-based cohort study of all HIV positive individuals aged ≥ 18 years residing in two cities where SUFA was operational using data from HIV clinics. We analysed data for one-year pre- and one-year post-SUFA implementation. We assessed the rates of enrolment in care, assessment for eligibility for antiretroviral therapy (ART), treatment initiation, loss to follow-up (LTFU) and mortality. Multivariate Cox regression was used to determine the pre-to-post-SUFA hazard ratio. Results A total of 2,292 HIV positive individuals (1,085 and 1,207 pre and post-SUFA respectively) were followed through their cascade of care. In the pre-SUFA period, 811 (74.6%) were enrolled in care, 702 (86.6%) were found eligible for ART, 485 (69.1%) initiated treatment, 102 (21%) were LTFU and 117 (10.8%) died. In the post-SUFA period, 930 (77%) were enrolled in care, 896 (96.3%) were found eligible for ART, 627 (70%) initiated treatment, 100 (16%) were LTFU and 148 (12.3%) dead. There was an 11% increase in the rate of HIV linkage to care (HR = 1.11; 95% CI 1.001, 1.22 p<0.05), a 13% increase in the rate of eligibility for ART (HR = 1.13, 95% CI 1.02,1.25, p<0.01) and a 27% reduction in LTFU (HR = 0.73, 95%CI 0.55, 0.97, p<0.05). Rates of ART initiation and mortality did not change. Conclusion SUFA was effective in improving HIV care in relation to linkage to care, eligibility and ART retention. Therefore, the scale up across the whole of Indonesia of the SUFA currently in the form of a test and treat policy, with improvement in testing and treatment strategies is justified.