Background Respiratory tract infections (RTI) are the second most frequent diagnosis after Malaria amongst Outpatients in Uganda. Majority are Non pneumonia cough and flu which are self-limiting and often do not require antibacterials. However, antibiotics are continuously prescribed for these conditions and are a major contributor to antimicrobial resistance and wastage of health resources. Little is known about this problem in Uganda hence the impetus for the study. Objectives To determine the antibacterial prescribing rate and associated factors among RTI outpatients in Mbarara municipality Methodology This was a retrospective cross-sectional study on records of RTI outpatients from 1st April 2019 to 31st March 2020 (prior to the novel corona virus disease pandemic) in four selected public health facilities within Mbarara municipality. A pretested data caption tool was used to capture prescribing patterns using WHO/INRUD prescribing indicators. We used logistic regression to determine factors associated to antibacterial prescribing. Results A total of 780 encounters were studied with adults (18-59 years) forming the largest proportion of age categories at (337, 43.15%) and more females (444, 56.85%) than men (337, 43.15%). The antibacterial prescribing rate was 77.6% (606) with Amoxicillin the most prescribed 80.4% (503). The prescribing pattern showed an average of 2.47 (sd 0.72) drugs per encounter and the percentage of encounters with injection at 1.5% (24). Drugs prescribed by generic (1557, 79%) and drugs prescribed from essential medicine list (1650, 84%) both not conforming to WHO/INRUD standard; an indicator of possible irrational prescribing. Female gender (adjusted odds ratio [aOR] = 1.51, 95% confidence interval [CI]: (1.06–2.16); 18–59 years age group (aOR = 1.66, 95% CI: 1.09–2.33) and Individuals prescribed at least three drugs were significantly more likely to have an antibacterial prescribed (aOR= 2.72, 95% CI: 1.86–3.98). Conclusion The study found a high antibacterial prescribing rate especially among patients with URTI, polypharmacy and non-conformity to both essential medicine list and generic name prescribing. This prescribing pattern does not comply with rational drug use policy and needs to be addressed through antimicrobial stewardship interventions, prescriber education on rational drug use and carrying out more research to determine the appropriateness of antibacterial prescribed.