BACKGROUND: There are few studies that characterize sex-related differences in HIV outcomes among adolescents and young adults (AYA) 15-24 years of age. METHODS: We conducted a retrospective cohort study among AYA who enrolled in a comprehensive HIV program in Mozambique between 2012-2016. We assessed patients by sex and pregnancy/lactation status, comparing time to combination antiretroviral therapy (ART) initiation using Cox proportional hazard models. We employed multivariable logistic regression to investigate pre- and post-ART retention. Patients were defined as 'retained pre-ART' if they attended at least 3 of 4 required visits or started ART in the 6 months after enrollment, and 'retained post-ART' if they had any ART pickup or clinical visit during the last 90 days of the one-year follow-up period. RESULTS: Of 47,702 patients in the cohort, 81% (n = 38,511) were female and 19% (n = 9,191) were male. Of the females, 57% (n = 21,770) were non-pregnant and non-lactating (NPNL) and 43% (n = 16,741) were pregnant or lactating (PL). PL (aHR 2.64, 95%CI:2.47-2.81) and NPNL females (aHR 1.36, 95%CI:1.30-1.42) were more likely to initiate ART than males. PL females had higher odds of pre-ART retention in care (aOR 3.56, 95%CI: 3.30-3.84), as did NPNL females (aOR 1.71, 95%CI: 1.62-1.81), compared to males. This was also true for retention post-ART initiation, with higher odds for both PL (aOR 1.78, 95%CI:1.63-1.94) and NPNL females (aOR 1.50, 95%CI:1.35-1.65) compared to males. CONCLUSIONS: PL females were most likely to initiate ART and remain in care post-ART in this AYA cohort, likely reflecting expansion of Option B+. Despite pregnancy and policy driven factors, we observed important sex-related disparities in this cohort. NPNL females were more likely to initiate ART and be retained in care before and after ART initiation than males. These data suggest that young males need targeted interventions to improve these important care continuum outcomes.