It has been known for a long time that the equatorial electrojet varies from day to day even when solar and geomagnetic activities are very low. The quiet time day-to-day variation is considered to be due to irregular variability of the neutral wind, but little is known about how variable winds drive the electrojet variability. We employ a numerical model introduced by Liu et al. (2013), which takes into account weather changes in the lower atmosphere and thus can reproduce ionospheric variability due to forcing from below. The simulation is run for May and June 2009. Constant solar and magnetospheric energy inputs are used so that day-to-day changes will arise only from lower atmospheric forcing. The simulated electrojet current shows day-to-day variability of ±25%, which produces day-to-day variations in ground level geomagnetic perturbations near the magnetic equator. The current system associated with the day-to-day variation of the equatorial electrojet is traced based on a covariance analysis. The current pattern reveals return flow at both sides of the electrojet, in agreement with those inferred from ground-based magnetometer data in previous studies. The day-to-day variation in the electrojet current is compared with those in the neutral wind at various altitudes, latitudes, and longitudes. It is found that the electrojet variability is dominated by the zonal wind at 100–120 km altitudes near the magnetic equator. These results suggest that the response of the zonal polarization electric field to variable zonal winds is the main source of the day-to-day variation of the equatorial electrojet during quiet periods.