In September 2009, tropical cyclone Ketsana brought record rainfall over Metropolitan Manila, Philippines, resulting in widespread flooding and incapacitated the city for days. The extensive damage caused by heavy rainfall events such as this highlights the need to have an effective weather prediction model to forecast these extreme events for the Philippines. As an initial step towards this goal, this study aims to examine the sensitivity of the rainfall simulation of the Weather Research and Forecasting (WRF) model to the physical parameterization schemes related to the planetary boundary layer (PBL) and microphysics processes. Comparison with observation data shows that the PBL scheme influences the spatial distribution of rainfall, whereas the microphysics scheme can affect rainfall magnitudes. The PBL scheme can also affect the intensity and track of the tropical cyclone as indicated in the surface latent heat flux and vertical velocity, as well as the magnitude of the mixing ratio of the different hydrometeors, which consequently affects the simulated rainfall. On the other hand, microphysics schemes can also influence the vertical distribution of each hydrometeor, likely due to differences in the treatment of ice phase processes and its interaction with the PBL scheme. Among the schemes tested, the model simulation using the ACM2 PBL and the WSM6 microphysics schemes captures this particular heavy rainfall event, in terms of spatial distribution, amount and timing. The results of this study show the importance of the PBL and microphysics schemes in simulating heavy rainfall, as well as the high potential of using WRF for future forecasts, especially for extreme weather events in the Philippines.