Background and aim Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, primarily caused by Enterobacteriaceae. The rise of carbapenem-resistant Enterobacteriaceae (CRE), complicates treatment of UTIs, yet the distribution of CRE and carbapenemase genes in Uganda's hospitals is not sufficiently explored. This study aimed to examine the distribution of carbapenemase genes in Enterobacteriaceae isolated from urinary tract infections in outpatients in southwestern Uganda. Methods A cross-sectional hospital-based study was conducted in southwestern Uganda. The study involved 111 participants who tested positive for carbapenemase genes. These participants were selected from a total of 2,371 patients presenting with urinary tract infections (UTIs) at Bwizibwera Health Center IV and Rubaya Health Center III. Enterobacteriaceaewere identified using a series of biochemical tests, and the presence of carbapenemase resistance genes (blaVIM, blaOXA-48, blaNDM, blaKPC, and blaIMP) was confirmed through polymerase chain reaction (PCR) genotyping. Data were analyzed and presented as frequencies and proportions, displayed in tables and charts. Results We screened a total of 2,371 participants with symptoms of urinary tract infections (UTI) for Enterobacteriaceae, 455 (19.2%) tested positive for at least one of the Enterobacteriaceae species. Disk susceptibility testing (DST) for carbapenems (meropenem and ertapenem) revealed a phenotypic carbapenem resistance prevalence of 5.7% (26/455), while polymerase chain reaction (PCR) identified a genotypic prevalence of 24.4% (111/455). . was the most common carbapenemase gene carrier (60/111, 54.1%), with blaIMP being the most frequent gene detected (32.4%). PCR detected more carbapenemase-producing organisms compared to DST. Notably, 14.4% of the isolates harbored multiple carbapenem resistance genes, with one sample carrying four different genes. Conclusion Our study revealed a high genotypic prevalence of CRE, especially in and isolates with a low phenotypic expression. This suggests that relying solely on DST could miss resistant strains, emphasizing the importance of molecular diagnostics like PCR for accurate detection. Carbapenemase inhibitors should be prescribed alongside carbapenem drugs where CREs are suspected, combined with continued surveillance to help manage CRE and reduce their spread in resource-limited settings.