Refugee HIV positive mothers experience significant obstacles in accessing, utilizing and adhering to antiretroviral therapy (ART). Identifying ART non-adherence can help in the development of interventions aimed at improving adherence and subsequently effectiveness of ART among the refugee mothers. We describe the use and the factors associated with non-adherence to ART among Refugee HIV positive pregnant mothers aged 18-49 years in Kyangwali Refugee Camp, Uganda. We conducted a cross-sectional study among HIV positive pregnant mothers aged 18-49 years in Kyangwali refugee camp between May and June 2023. Using a structured questionnaire, we collected data on use, and factors associated with non-adherence to ART. We used modified Poisson regression analysis to determine factors associated with non-adherence to ART. Of the 380 participants enrolled, 192 (50.5%) were married, mean age 32.1 years. Overall, 98.7; 95% Confidence Interval (CI) [97.5-99.8%] were using ART and 27.4; 95% CI [22.9-31.9%] were non-adherent. Non-adherence was associated with: Initiating Prevention of Mother to Child Transmission (PMTCT) care in the third trimester of pregnancy (adjusted Prevalence ration(aPR): 2.06; 95% CI: 1.27-3.35), no need to get permission to seek PMTCT services aPR 1.61; 95% CI [1.07-2.42] and poor attitude of PMTCT providers aPR 1.90; 95% CI [1.20-3.01]. Non-adherence to ART was generally high; therefore limiting the effectiveness of the PMTCT program in this setting. Refugee context specific education interventional programs aimed at early initiation into HIV care, strong social and psychological support from families, communities and health care providers are vital to improve adherence in this setting.