Abstract The structure and variations of the North Equatorial Counter Current (NECC) in the far western Pacific Ocean during 2014-2016 are investigated using repeated in-situ hydrographic data, altimeter data, Argo data, and reanalysis data. The NECC shifted ~1 degree southward and intensified significantly with its transport exceeding 40 Sv (1 Sv = 10 6 m 3 s -1 ), nearly double its climatology value, during the developing phase of the 2015/16 El Niño event. Observations show that the 2015/16 El Niño exerted a comparable impact on the NECC with that of the extreme 1997/98 El Niño in the far western Pacific Ocean. Baroclinic instability provided the primary energy source for the eddy kinetic energy (EKE) in the 2015/16 El Niño, which differs from the traditional understanding of the energy source of EKE as barotropic instability in low latitude ocean. The enhanced vertical shear and the reduced density jump between the NECC layer and the subsurface North Equatorial Subsurface Current (NESC) layer renders the NECC–NESC system baroclinically unstable in the western Pacific Ocean during El Niño developing phase. The eddy-mean flow interactions here are diverse associated with various states of the El Niño Southern Oscillation (ENSO).