Regional climate models have been useful in climate studies and in downscaling climate projections from global climate models, especially for areas characterized by complex topography and coastline features, such as the Philippines. However, several factors may affect model skill, such as uncertainties related to the boundary conditions and model configuration. This study evaluates the performance of the non-hydrostatic regional climate model (NHRCM) over the Philippines. Present-day climate simulations at 50 km resolution are conducted using two sets of boundary conditions (ECMWF ERA-Interim and the NCEP/NCAR Reanalysis Project NNRP1), as well as two convective parameterization schemes in the model (Grell and Kain-Fritsch). Results show that the seasonal changes in the spatial distribution of temperature, rainfall, and winds over the Philippines are simulated reasonably well. NHRCM has an overall cold and dry bias over land, the degree of which depends on the boundary condition and the convective scheme used. After adjusting the simulated temperature because of the difference in topography, the temperature differs from that observed by -0.90°C to -0.42°C on average. The rainfall bias in NHRCM ranges from -62.13 % to -25.20 %. Regardless of the boundary condition, the Grell scheme results in the lowest temperature bias with high skill scores, while the Kain-Fritsch scheme gives the lowest rainfall bias with high correlation and skill scores. The boundary conditions also influence model skill, such that the model bias is lower for temperature when ERA-Interim is used, but lower for rainfall with NNRP1. NHRCM represents the seasonal cycles of temperature and rainfall for all regions, but tends to generate more occurrences of cold and dry months. Improvements in the model are still possible, but these results indicate the potential of the model to be used for providing essential information for describing historical and future changes in the Philippine climate.