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Adolescent sexual and reproductive health and rights remain critical public health issues in low- and middle-income countries, with adverse health, educational, and economic consequences. Uganda faces significant challenges with high rates of unintended pregnancies among adolescents. This study examined factors associated with unintended pregnancies among unmarried adolescents in Eastern Uganda. A cross-sectional study was conducted among unmarried adolescent boys and girls aged 15–19 years in Iganga and Bugiri municipalities between February and March 2024. Data were collected at mobile money shops to target customers through face-to-face interviews using a structured questionnaire. The variables included sociodemographic characteristics, sexual behaviors, contraceptive knowledge, usage of mobile money shops, and environmental factors. Multivariate logistic regression was applied to identify factors associated with unintended pregnancies. Among the 1267 eligible adolescents, 876 had ever engaged in sexual intercourse. Of these, 22.5% (n = 197) reported experiencing an unintended pregnancy. The factors associated with a lower likelihood of pregnancy included school enrollment (adjusted odds ratio [AOR] = 0.36; 95% confidence interval [CI]: 0.24–0.54), co-residences with parents (AOR = 0.48; 95% CI: 0.33–0.69), and teachers’ awareness of students’ lives/worries (AOR = 0.56; 95% CI: 0.37–0.84). Factors associated with a higher likelihood of pregnancy were knowledge of how to use contraceptives (AOR = 2.28; 95% CI: 1.16–4.49), communication with parents/guardians (AOR = 1.91; 95% CI: 1.32–2.75), parental support for contraception (AOR = 1.64; 95% CI: 1.03–2.59), and mobile phone possession (AOR = 2.31; 95% CI: 1.09–4.90). Adolescents who had experienced pregnancy were significantly more likely to consider community-based distributors as comfortable sources for sexual and reproductive health information (AOR = 1.72; 95% CI: 1.11–2.66) and contraceptives (AOR = 4.76; 95% CI: 2.39–9.47). Nearly one-quarter of unmarried adolescents have experienced—or caused—a pregnancy in Eastern Uganda. School enrollment and parental engagement were inversely associated with adolescent pregnancy. Many adolescents may gain contraceptive knowledge and support after an unintended pregnancy. Community-based service delivery was preferred over facility-based options. Further researches are needed to develop a community-based platform for reaching underserved unmarried adolescents and promoting appropriate contraceptive use. This study was registered at Japan’s University Hospital Medical Information Network (UMIN000053332) on 12 January 2024. Adolescent sexual and reproductive health and rights (SRHR) are pressing public health issues globally. Uganda has a high rate of unintended pregnancies among adolescents. This study examined factors associated with unintended pregnancies among unmarried adolescents in Eastern Uganda. This cross-sectional study was conducted in two municipalities (Iganga and Bugiri) in Eastern Uganda. It included 1267 unmarried boys and girls aged 15–19 years who visited mobile money shops. Among the 876 adolescents who had ever had sexual intercourse, 22.5% of them experienced pregnancies. The factors associated with a lower prevalence of pregnancy were: school enrollment (adjusted odds ratio [AOR] = 0.36), co-residence with parents (AOR = 0.48), and teachers’ awareness of students’ lives/worries (AOR = 0.56). In contrast, the factors associated with a higher prevalence of pregnancy were: knowledge of how to use contraceptives (AOR = 2.28), communication with parents/guardians (AOR = 1.91), parental support for contraception (AOR = 1.64), and mobile phone possession (AOR = 2.30), which may imply that many adolescents gained contraceptive knowledge and support only after an unintended pregnancy. In addition, community-based distributors, such as a mobile money shop, were considered comfortable channels for receiving SRHR services. In conclusion, it was suggested that school enrollment and parental engagement were positively associated with lower prevalence of unintended pregnancy, and many adolescents gained contraceptive knowledge and support only after an unintended pregnancy. Community-based service delivery was preferred over conventional facility-based options. Further researches are needed to develop a community-based platform for reaching out to underserved unmarried adolescents and promoting appropriate contraceptive use.