Simulating the ground motions of future earthquakes requires a proper understanding and modeling of source, path, and site effects. Ground motions recorded during recent earthquakes very close to their ruptured faults provide new evidence of the importance of source effects and suggest that physics‐based rupture modeling is critical to account for them. Here, we develop dynamic rupture models to simulate the near‐fault ground motions generated by the 2016 Kumamoto, Japan, earthquake ( 7.0) at Nishihara village, which feature a large‐amplitude velocity pulse. Comparison of mainshock and foreshock waveforms suggests that the source of the velocity pulse is on the Futagawa fault segment located very close to the site. Our dynamic models use the spectral element method and are built upon a previous kinematic description of the event via a so‐called “characterized source model,” with three strong‐motion generation areas (SMGAs) on the assumed fault plane. We first develop a reference model that reproduces the main features of the rupture process in agreement with previous results of kinematic source inversion. We then examine the sensitivity of the simulated near‐fault ground motions to the frictional parameters (critical slip‐weakening distance and stress drop) in the shallow part of the fault and to the geometrical properties of the shallow SMGA. Even assuming drastically different frictional properties in the shallow part of the fault, the amplitude of the simulated ground motions was affected little. On the other hand, changes of geometrical properties of the shallow SMGA generated large differences in simulated ground motions. The results indicate that geometrical features of the shallow SMGA played a more important role in generating near‐fault ground motions with velocity pulses as observed at Nishihara village during the 2016 Kumamoto earthquake.