Long-term reanalysis data were used to assess inter-decadal to decadal modulations of the North Equatorial Current (NEC) bifurcation in the Pacific after the early 1990s. The wind stress curl anomaly (WSCA) in the region of 10° N–15° N and 160° E–170° E (C-BOX) had been found to excite Rossby waves and control NEC bifurcation along the Philippine coast. Our analysis revealed that the WSCA in the C-BOX has been remotely modulated by the Southern Annular Mode (SAM) since the early 1990s. It is shown that the SAM shifted to its positive phase at this transition and began strongly impacting the WSCA in the C-BOX and the NEC bifurcation. During the positive SAM phase after the early 1990s, strong climate variability occurred in the tropical to subtropical area of the North Pacific, with a clear footprint connected to the Antarctic region. Consistent with that finding, we determined that during the positive SAM phase, a dipole sea surface temperature pattern was generated in the South Pacific; this induced an atmospheric Rossby wave train in upper-level wind shear that propagated northward to the North Pacific. Such effects further enhanced downward motion and divergence at the surface, intensifying the easterlies in the equatorial area and the anticyclonic WSCA in the C-BOX. The anticyclonic WSCA in the C-BOX substantially excited downwelling oceanic Rossby waves at the surface, inducing an equatorward trend of NEC bifurcation after the early 1990s.