Background There is growing evidence of associations between extreme weather events (EWE) and HIV vulnerabilities, yet this is understudied in humanitarian settings. We examined associations between EWE and HIV vulnerabilities among refugee youth in Bidi Bidi Refugee Settlement, Uganda. Methods We collected baseline (February to March 2024) cohort data with refugee youth aged 16-24years in Bidi Bidi. We conducted linear and logistic regression to assess associations between (a) number of past-year EWE types (e.g. extreme rain/flooding, changes in expected rain patterns, drought, extreme heat, fire, changes in expected temperature), and (b) frequency of past-year EWE, with HIV vulnerabilities (sexual relationship power, reproductive autonomy, condom use self-efficacy, transactional sex, intimate partner violence, multiple sex partners), adjusted for age, gender, education and employment. Results Among 400 participants (50% women; mean age: 19 years, standard deviation: 2.3), a higher number of past-year EWE types (vs 1) was significantly associated with reduced sexual relationship power (2-4 EWE: adjusted beta [aβ] = -2.96, P =0.009; ≥5 EWE: aβ = -4.92, P P =0.006; ≥5 EWE: aβ = -0.42, P =0.001) and condom use self-efficacy (2-4 EWE: aβ = -3.02, P P P =0.040), intimate partner violence (≥5 EWE: aOR 3.13, P =0.007) and multiple sex partners (≥5 EWE: aOR 4.70, P =0.002). Increased EWE frequency was significantly associated with lower sexual relationship power, reproductive autonomy and condom use self-efficacy. Conclusions EWE experiences were associated with multiple HIV vulnerabilities among refugee youth. Climate-informed, youth-tailored HIV prevention strategies are urgently needed.