This study investigates the interannual variations in the North Equatorial Counter Current (NECC) associated with the eastern Pacific and the central Pacific types of El Niño. Using observational analysis and ocean simulations, we show that the wind stress anomalies during the two El Niño types are of comparable amplitude but have different spatial structures, which results in significant and distinct variations in the NECC. The NECC shifts southward and intensifies during the developing phase of El Niño, but the variations are confined in the central eastern Pacific for the eastern Pacific type and the western central Pacific for the central Pacific type. These differences can be attributed to modulations in equatorial Kelvin wave and tropical Rossby wave propagation as well as Ekman pumping.