Objectives Uganda adapted its policy for prevention of vertical transmission (VT) of HIV transmission as the World Health Organization released Options A, B and B+. We assessed trends in diagnostic testing, breastfeeding practices, maternal and infant antiretroviral therapy (ART), mortality, VT and HIV‐free survival (HFS) among Ugandan infants born to women living with HIV during this period of successive guideline changes. Methods This is is a retrospective observational study of infants attending early infant diagnosis clinics at two Ugandan hospitals. Results A total of 1885 infants (48% female) were managed from 2009 to 2017. DNA polymerase chain reaction (PCR) for early infant diagnosis was performed on 1719 infants (92%, one or more PCR tests) and 676 infants (36%, two PCR tests). HIV serology was performed on 90 infants (4.8%). Testing increased over the study period but remained suboptimal, due to high loss to follow‐up (LTFU). A total of 93% of infants were breastfed, for a median of 9.5 months. The duration of breast milk exposure increased over the study period, consistent with guidelines that increasingly encouraged breastfeeding. Nine cases (0.48%) of suspected breast milk transmission were observed. The use of ART increased significantly over the study period. Mortality (3.5%, 2.7% and 1.1%; p = 0.0076) and VT (17%, 12% and 7.4%; p < 0.0001) decreased over the study period (2008–2010, 2011–2012 and 2013–2017, respectively). LTFU values were 31%, 49% and 59% at 6, 12 and 18 months of age, respectively, with only modest improvements over time. HFS could only be conclusively documented in 532 infants (28%) because of LTFU. Conclusions From 2009 to 2017, outcomes improved among HIV‐exposed infants in Uganda. LTFU remains a barrier to optimal care.