Intraseasonal vertical velocity variation in the central equatorial Indian Ocean was investigated using observations from the field experiment “Mirai Indian Ocean Cruise for the Study of the MJO-convection Onset” and from the Research Moored Array for African-Asian-Australian Monsoon Analysis and Prediction, in October-November 2006. Using an array of four subsurface moored acoustic Doppler current profilers, we estimated vertical velocity by applying the continuity equation. Results indicated alternating downwelling and upwelling episodes at around thermocline depth, with maximum amplitudes larger than 8.0 × 10−5 m s−1, or about 7 m per day. The vertical velocity variation was mainly produced by the divergence/convergence of meridional currents, with a quasi-biweekly period of 11–16 days. The temporal changes in temperature around thermocline depth were consistent with variations in vertical velocity, whereas upwelling had less impact on the surface layer temperature. Intraseasonal variations in the ocean may be a part of biweekly fluctuations by remotely forced mixed Rossby-gravity waves, which have a meridional current maximum at the equator, accompanied by divergence/convergence in the surface layer a few degrees from the equator.