The effects of geomagnetic activity on the equatorial neutral thermosphere are investigated with mass spectrometer measurements from the Atmosphere Explorer E (AE‐E) satellite and simulations generated by the National Center for Atmospheric Research thermosphere/ionosphere general circulation model (TIGCM). A study of the local time dependence of the equatorial geomagnetic storm response concentrates on a disturbed period from March 20 (day 79) to March 31 (day 90), 1979. This interval was the subject of an intense data‐gathering and analysis campaign for the Coordinated Data Analysis Workshop 6, and global TIGCM predictions are available for the specific conditions of the storm as a function of universal time. The AE‐E measurements demonstrate that significant geomagnetic storm‐induced perturbations of upper thermospheric N2 and O densities extend into the equatorial zone but are mainly restricted to the midnight/early morning sector. The qualitative features of the observations are reproduced by the TIGCM, although in general, the model simulations overestimate the storm temperature and density enhancements, primarily in the nighttime thermosphere. This suggests that either the nighttime cooling rates in the TIGCM are too small or that the specified auroral forcings of the model are too persistent.