Background The desire to have children among mothers living with HIV remains a serious public health issue in nations with low coverage for antiretroviral therapy and the prevention of mother-to-child transmission, even if it is feasible to have an HIV-negative child. Therefore, this study aimed to assess fertility desire and associated factors among antiretroviral therapy-attending HIV-positive women at Hiwot Fana Specialized University Hospital, in Harari, Ethiopia. Methods A facility-based cross-sectional study design was employed among 639 anti retro-viral therapy attending HIV - positive women by systematic random sampling method selected from June 15 to November 30, 2020. A binary logistic regression model was fitted to identify the associated factors with fertility desire. Descriptive results were presented in percentages, whereas analytical results were reported in adjusted ORs (AORs) with a 95% CI. At p=0.05, statistical significance was declared. Results A total of 639 participants were included in the study; 69.5%(95% CI 65.7 to 72.9%) of the participants had fertility desire. Younger age (<35 years) (AOR=2.35, 95% CI 1.27 to 4.35), married women (AOR=3.02, 95% CI 1.32 to 12.25), childless women (AOR=2.86, 95% CI 1.17 to 4.82) and women whose duration of HIV diagnosis was ≤5 years (AOR=0.41, 95% CI 0.20 to 0.71) were significantly associated with fertility desire. Conclusion The majority of the study participants have a desire to have children. In light of the high prevalence of fertility desire among antiretroviral therapy-attending HIV-positive women, it is recommended to counsel younger women on reproductive planning and encourage partner testing.