Background: Previous research shows that gendered differences in time use unfairly impact women’s career advancement and influence workforce management. Despite a growing body of literature on gendered time use, the topic has not been well documented among specializing medical doctors in sub-Saharan African countries, including Uganda. Objectives: This study was conducted among specialist medical doctors at Makerere University to: (i) analyze gendered differences in time use for paid and unpaid activities and (ii) assess whether parenting influences time use. Methods: The study sample comprised 244 medical doctors pursuing graduate specialist programs in 2024. The data collection, which utilized a self-administered questionnaire, assessed socio-demographic factors and self-reported time spent on paid work, unpaid domestic work, unpaid care for household members, studying, socializing, and leisure activities. Quantile regression analysis, with 95% confidence intervals, was used to compare median differences in reported time use across various activities for men and women. Results: Compared to men, women reported spending more time on unpaid domestic work (2 vs 1 h/day: 95% CI: 0.6, 1.4) and less time on leisure activities (4 vs 7 h/week: 95% CI: −5.3, −0.8). Women with children spent more time on paid work than their male counterparts. Women with children reported spending half a day more on paid work and an additional hour on unpaid domestic work compared to men with children. Conclusion: This gender imbalance in time use could negatively impact the career progression and well-being of female doctors and further reinforce gender inequalities in the medical workforce in Uganda.