Background: Obesity is common among people living with HIV (PLWH) and early-stage infection, yet associations with combination antiretroviral (cART) adherence are unclear. Methods: Among PLWH initiating cART in Uganda and South Africa, body mass index (BMI) was assessed at cART initiation, and cART adherence was monitored in real-time over 12 months. The association of obesity (BMI ≥ 30 kg/m2) with adherence was assessed among nonpregnant participants with CD4 > 350 cells/mm3 using fractional regression modeling. Results: Among 322 participants, median age was 32 years, 70% were female, and 54% were from Uganda. Prevalence of obesity was 12% in Uganda and 28% in South Africa. Mean overall cART adherence was 83% in Uganda and 66% in South Africa. Participants with obesity had higher adherence than those without obesity: +3.6% (p = 0.44) in Uganda and +11.4% (p = 0.02) in South Africa. Conclusion: Obesity at cART initiation was common and associated with higher adherence, although only significantly in South Africa.