Punching shear failure in slab-column connections is a brittle collapse mode that threatens the safety of flat reinforced concrete (RC) slabs. Conventional design provisions are generally conservative but exhibit inconsistencies across geometric and material variations. This study develops an eXtreme Gradient Boosting (XGBoost) model to predict the ultimate punching shear capacity of flat RC slabs, using a database of experimental results categorized by four different geometric domains, including square slab with square column, circular slab with circular column, square slab with circular column, and circular slab with square column, covering the geometric, materials strength, and reinforcement properties of input parameters. The model achieved high predictive accuracy across the domains with coefficient of determination (R2) values > 0.930 in unseen testing datasets with minimal bias (0.994–1.006) and reduced scatter. Model interpretability, addressed through the SHapley Additive exPlanations analysis, confirmed slab thickness and average effective depth as the most critical predictors of shear capacity, followed by concrete strength and reinforcement parameters, while boundary condition parameters showed negligible influence due to the predominance of interior column cases. These findings demonstrate that XGBoost provides accurate, reliable, and interpretable predictions of punching shear capacity, offering a data-driven alternative to code-based methods and supporting safer and more consistent design of flat RC slabs.