Sub-Saharan Africa bears the highest burden of HIV/AIDS infections and constitutes 72% and 69% of AIDS-related deaths and people living with HIV worldwide, respectively. Due to the relationship between pulmonary infections and HIV/AIDS, it is biologically plausible that the surge in morbidity and mortality among HIV/AIDS patients could be attributed to an increase in pulmonary infections among this cohort of patients. This study determined the bacterial profile, susceptibility patterns, and factors associated with culture-positive sputum among HIV patients presenting with cough at the Lira Infectious Disease Centre in Northern Uganda. This prospective cross-sectional study recruited 180 participants. Culture and sensitivity of the sputum samples were done to determine the causative organism and its susceptibility. Blood agar, MacConkey's agar, and Chocolate agar were deployed for the culture media. Antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion test. Data were analyzed using SPSS version 26. Out of the 180 enrolled patients, 113 were females with a mean age of 45. Bacterial growth was seen in 56 of the 180 samples. The most common isolate was Staphylococcus aureus at 35.7% of the 56 growths. The minority that accounted for 1.8% each were Citrobacter freundii, Salmonella species and Acinetobacter baumanii, respectively. A combination of ceftriaxone and gentamicin was effective against most organisms isolated in this study. At the multivariate level of analysis, an unsuppressed viral load and low peripheral oxygen saturation were independently associated with a sputum culture-positive cough. HIV patients at LIDC who present with productive cough with low oxygen saturation and an unsuppressed viral load may be screened for Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumonia, Klebsiella pneumonia, and Enterobacter species infection. A combination of ceftriaxone and gentamicin may be used as empiric therapy before the culture and sensitivity results are available.