The zonal velocity produced by a Regional Ocean Modeling System (ROMS)‐based Pacific Ocean circulation model was validated against in situ measurements along the 137°E longitude. The Pacific model successfully reproduced the position and the shape of the North Equatorial Current (NEC) as well as the latitude of maximum surface velocity in the NEC region (8–17°N). The flow field produced by the Pacific model was then used to conduct numerical Lagrangian experiments, in which passive particles were released along a transect (142.5°E, 12.5–17°N) that traverses the known Japanese eel spawning area, and the effects of NEC strength and bifurcation latitude on the particle advection in the northwest Pacific were studied. Our results suggest that, in the 20‐yr period (1993–2012), the variability of the currents alone can cause interannual variability of one order of magnitude in the Kuroshio Entrance (KE), the percentage of particles entering the Kuroshio, the range of which varies from 43% in 1997 to 6% in 2012. The yearly‐averaged KE is not sensitive to the NEC bifurcation latitude. Instead, it is controlled by the average zonal velocity of a fixed domain (125–143°E, 13.5–17°N) and related to a recently‐developed climate index, the Philippines–Taiwan Oscillation (PTO). During the positive phase of the PTO, the zonal velocity in the domain, hence the yearly‐averaged KE, increases, and the opposite is true in the negative phase of the PTO. Considering only the trajectories, diel vertical migrations (DVM) in the top 400 m do not significantly affect Japanese eel larval transport, as incorporating DVM schemes does not increase the KE.