Background Opportunistic infections are late complications of HIV infection is the depletion of the immune system. It is a major public health problem and high morbidity AIDS patients die of AIDS-related infections in developing countries like Ethiopia. Identification of opportunistic infections (OIs) is important to develop a specific intervention. Therefore, this study aimed to assess the burden and associated factors of opportunistic infections.Method A facility-based cross-sectional study was conducted on 420 randomly selected HIV/AIDS patients taking anti-retroviral therapy. Data was collected from selected hospitals in Sidama Zone based on population proportion to size. Data was collected by a pre-tested questionnaire and a pre-tested checklist from the medical records of patients. Data entry and analyzed for descriptive and logistic regression models by SPSS v.23. The result declared as statistically significant at p < 0.05.Result The magnitude of opportunistic infections was 39.6%. Major identified OIs was oral candidacies 23.2%, recurrent bacterial pneumonia 21.5%, Herpes zoster 6.3%, and Pulmonary Tuberculosis 6.0%.The magnitude of opportunistic associated with; older age [AOR=2.69, 95% CI: 1.33-5.43], No formal education [AOR=3.12, 95% CI: 1.06-9.25], Low monthly income [AOR=2.27, 95%CI:1.35-3.83], initial CD4 count less than 200 cells/mm3 [AOR=1.91, 95% CI:1.05-3.46), WHO clinical stage II [AOR=2.43, 95% CI:1.34-4.42] and stage III and IV [AOR=4.27, 95% CI: 2.12-8.59], had no extra medicine additional to ART (prophylaxis) had [AOR= 5.91, 95% CI: 3.31-10.56], who interrupt ART medicines [AOR=2.03, 95% CI: 1.09- 3.80] and Khat chewing [AOR=5.48, 95% CI: 2.32-12.96] when compared to their counterparts.Conclusions The overall magnitude of opportunistic infections was high when compared with other studies. Health officials and clinicians need to give attention on the strengthening of the provision if ART with prophylaxis on early-stage and adhrerence, implementation of the TB/HIV collaboration activity, and early initiation of ART to reduce opportunistic infections.