Background Stigma towards sexually active young people presents profound barriers to uptake of sexual and reproductive health (SRH) services, including HIV testing and contraception. Yet, few studies have examined adolescent SRH stigma trajectories over time. To address this knowledge gap, we examined associations between social-ecological factors and trajectories of adolescent SRH stigma among urban refugee youth in Kampala, Uganda. Methods This longitudinal cohort study with refugee youth in Kampala collected data on adolescent SRH stigma at four time-points between 2022 and 2024. We used latent class growth analyses to examine distinct trajectories of adolescent SRH stigma, and examined baseline social-ecological and socio-demographic factors associated with class membership using multivariable logistic regression. Results Among the participants (n = 164 with n = 668 observations; mean age 19.9 years, standard deviation 2.5 years; 52.8% cisgender women), we categorised two distinct adolescent SRH stigma trajectories: consistently high (n = 496; 74.2%) and sustained low (n = 172; 25.8%). In multivariable analyses, living in Uganda ≥1 year at baseline assessment (1–5 years: adjusted odds ratio [aOR] 5.28, confidence interval [CI] 2.29–12.19, P < 0.001; 6–10 years: aOR 6.20, CI 2.61–14.69, P < 0.001; or >10 years: aOR 3.89, CI 1.56–9.68, P < 0.01) compared with <1 year, unemployment (aOR 1.62, CI 1.02–2.56, P < 0.05), having children (aOR 2.84, CI 1.30–6.21, P < 0.05), past 3-month multiple sexual partners (aOR 6.14, CI 1.73–21.75, P < 0.01) and higher depression symptoms (aOR 1.04, CI 1.01–1.08, P < 0.01) were associated with the consistently high (vs sustained low) adolescent SRH stigma trajectory. Conclusions Social-ecological and socio-demographic factors were associated with consistently high levels of adolescent SRH stigma over 2 years. Multi-level strategies can meaningfully engage youth in developing stigma reduction strategies for SRH service delivery.