Introduction Family Planning (FP) is a life-saving, empowering and cost-effective interventions for women and girls. Access to FP is still challenging to female refugees due to several barriers including language, low educational level, lack of information, influence by significant others, limited income, desire to replace lost family members, moral values, cultural and religious norms as well as personal experience with contraceptives side effects. This study explored barriers to contraceptive use among South Sudan refugee women living in Adjumani district, Uganda. Methods An exploratory design using qualitative method was employed involving women between the ages of 15- 49 years. Purposive sampling was employed to select participants for Focus Group Discussions (FDGs) and In-depth Interviews (IDIs). Ten FDGs were conducted, each consisted of 6 to 8 participants. Two groups of females (15-19 and 20+ years) were reached. Twenty-seven IDIs were conducted with two similar categories as above. The In-depth interview and focus group discussion guides were used to collect data. The interviews were recorded verbatim and transcribed before being translated back to English from the local language. Audio recordings from the FGDs and IDIs were labelled, transcribed verbatim and translated into English. Deductive, team-based coding was implemented for codebook development, Transcripts were entered, and data coded using Atlas ti version 14. Data was analyzed using content analysis to produce the final outputs for the study. Results The study found that several challenges to contraception use included gender dynamics, socially constructed myths on contraceptive use, cultural norms related to contraceptive use, limited knowledge about contraceptive use, men’s negative attitudes, antagonism of contraceptive use by leaders and reprisal of women who use contraception. Conclusion The study concluded that there is need for community strategies to break down the barriers to contraception utilization among refugee women. Such strategies should include men and women alongside gatekeepers to enhance sustainability.