Extraordinarily poor recruitment of Japanese eels in East Asia has been generally reported during extreme El Niño years. However, the scenario failed to take place during the 2015-16 extreme event. In this study, we examined possible factors responsible for differing eel abundance in East Asia during the two strongest recent extreme El Niños, which occurred in 1997-98 and 2015-16. Numerical tracer experiments were carried out to determine why the impacts on eel catches seen in 1997-98 were not repeated in 2015-16. Among physical factors, two scenarios are likely responsible for extremely poor recruitment in East Asia: southward migration of the North Equatorial Current (NEC) or southward movement of eel spawning grounds. Comparing the latitudinal shift of NEC locations between the 1997-98 and 2015-16 El Niños, we conclude that NEC migration may be a factor, but is not chiefly responsible, for lower eel catches. Our findings pointed to southward movement of spawning grounds as the dominant factor. The northward movement of spawning grounds during 2015-16 meant that eel larvae were preferentially transported into the NEC-Kuroshio system, which resulted in a higher rate of recruitment success. The distinct evolution and dynamics of these two El Niño events led to different spawning ground locations, impacting eel abundance in East Asian countries.