Strong modulation of turbulent mixing by a westward‐propagating tropical instability wave (TIW) was observed in the stratified shear layer between the equatorial undercurrent (EUC) and the surface mixed layer during October and November 2008 at 0°N 140°W. The unique deep diurnal‐cycle mixing in the stratified layer beneath the equatorial cold tongue was observed where nighttime turbulent mixing was a factor of 10 greater than during daytime. The turbulent kinetic energy dissipation rate, ε, was Ο(10−6) W kg−1, and the turbulent heat flux was ∼−500 W m−2, at least 5–10 times greater than observed previously in the central equatorial Pacific. Turbulence mixing varied significantly during the four distinct phases of the meridional flow associated with the TIW. Observations during the northward‐to‐southward transition recorded the largest values of reduced shear squared, the thickest nighttime surface mixed layer, the deepest penetration of the deep‐cycle turbulence, and the largest turbulent heat flux and largest integrated ε in the deep‐cycle layer (DCL). During steady southward flow, the depth of the bases of the nighttime surface mixed layer and of the DCL were the shallowest. A 50‐m‐thick layer of strong turbulence was observed immediately above the EUC core during the northward‐to‐southward and steady southward phases. Here, the average ε exceeded 10−6 W kg−1, the eddy diffusivity exceeded 10−3 m2 s−1, and the turbulent heat flux was ∼−500 W m−2. To parameterize mixing in the central equatorial Pacific accurately, numerical models must simulate the enhancement of mixing associated with TIWs and also the variability of mixing in different TIW phases.