Background Humanitarian crises and migration make girls and women more vulnerable to poor sexual and reproductive health (SRH) outcomes. Nevertheless, there is still a dearth of information on SRH outcomes and access to SRH services among refugee girls and young women in Africa. We conducted a mixed-methods study to assess SRH experiences, knowledge and access to services of refugee girls in the Nakivale settlement, Uganda. Methods A cross-sectional survey among 260 adolescent girls 13–19 years old was conducted between March and May 2018. Concurrently, in-depth interviews were conducted among a subset of 28 adolescents. For both methods, information was collected regarding SRH knowledge, experiences and access to services and commodities. The questionnaire was entered directly on the tablets using the Magpi® app. Descriptive statistical analysis and multinomial logistic regression were performed. Qualitative data was transcribed and analysed using thematic content analysis. Results A total of 260 participants were interviewed, with a median age of 15.9 years. The majority of girls were born in DR Congo and Burundi. Of the 93% of girls who had experienced menstruation, 43% had ever missed school due to menstruation. Regarding SRH knowledge, a total of 11.7% were not aware of how HIV is prevented, 15.7% did not know any STI and 13.8% were not familiar with any method to prevent pregnancy. A total of 30 girls from 260 were sexually active, of which 11 had experienced forced sexual intercourse. The latter occurred during conflict, in transit or within the camp. A total of 27 of 260 participants had undergone female genital mutilation (FGM). The most preferred sources for SRH information was parents or guardians, although participants expressed that they were afraid or shy to discuss other sexuality topics apart from menstruation with parents. A total of 30% of the female adolescents had ever visited a SRH service centre, mostly to test for HIV and to seek medical aid for menstrual problems. Conclusions Adolescent refugee girls lack adequate SRH information, experience poor SRH outcomes including school absence due to menstruation, sexual violence and FGM. Comprehensive SRH services including sexuality education, barrier-free access to SRH services and parental involvement are recommended.