The outstanding mechanical properties of ultra-high-performance fiber-reinforced concrete (UHPFRC) can be used to improve the punching behavior of new slab-column connections. This study investigates the punching capacity of flat slab-column connections built with a rational combination of normal strength concrete (NSC) and UHPFRC in critical shear regions through non-linear finite element analyses (NLFEA) and by a punching shear model based on the critical shear crack theory (CSCT). Ten control tests from the literature were used to validate the Finite Element Models (FEM) developed to capture the behavior of slab-column connections made entirely with NSC, UHPFRC, and a combination of both materials. Parametric analyses were performed to investigate the behavior of connections with the rational use of UHPFRC, varying the reinforcement ratio, area, and thickness of the UHPFRC layer. The results indicated that placing a UHPFRC layer near the column in the slab compression zone significantly increases the punching capacity and deformation capacity compared to placing UHPFRC on the tensile side. The punching capacity enhancements varied between 26% and 156%, according to the reinforcement ratios and configurations of the UHPFRC layer investigated. The mean ratio between predicted punching capacities by advanced NLFEA and the analytical method proposed was 1.09, with a coefficient of variation of 10.3%. Therefore, the results indicated that the design of flat slabs with UHPFRC at the critical shear regions is a viable solution. Finally, the CSCT model can be used in design to predict the punching capacity of these connections.