Prospective investigations from sub-Saharan Africa on metabolic complications in youth with perinatally acquired HIV (PHIV) are lacking. We investigated the changes in insulin resistance in Ugandan PHIV on ART and uninfected controls and their relationship with inflammation, HIV, and cardiovascular disease (CVD) risk factors. Participants 10–18 years of age were included in a prospective study performed in Kampala, Uganda. We compared baseline and changes in insulin resistance (by HOMA-IR) and in markers of inflammation at baseline and 96 weeks. PHIVs were on ART with HIV-1 RNA level 400 copies/ml or less. Generalized Estimating Equation models were used to assess associations between HOMA-IR, and demographic as well as inflammatory markers. Of the 197 participants recruited at baseline (101 PHIV, 96 HIV-negative), 168 (89 PHIV, 79 HIV-negative) had measurements at 96 weeks. At baseline, median (Q1, Q3) age was 13 years (11,15), 53.5% were women, median CD4⁺ cell counts were 988 cells/μl (631, 1310). At baseline, HOMA-IR was significantly higher in PHIV than in controls (P = 0.03). HOMA-IR did not significantly change by week 96 in either group, and at 96 weeks, was similar between groups (P = 0.15). HOMA-IR was not associated with any inflammatory markers, or any specific ART. In longitudinal analysis, age and Tanner stage remained associated with higher HOMA-IR throughout the study period, after adjusting for HIV status. In this longitudinal cohort of virally suppressed PHIV in Uganda, PHIV have decreased insulin sensitivity compared to controls, however this difference does not persist through adolescence. ART and immune activation do not appear to affect glucose homeostasis in this population.