Abstract The upper‐atmosphere cooling trend is well documented, while the long‐term trend of the ionospheric electrodynamics remains poorly understood. Using two geomagnetic observation data sets over Indian sector, we analyze the long‐term trend of the monthly‐median equatorial electrojet (EEJ) in 1967–2015 after removing the solar activity and seasonal signals. During 1967–1999, a period of slow geomagnetic‐equator motion, the residual of the EEJ shows a decreasing trend between 09 and 13 LT and an increasing trend between 13 and 16 LT. Following accelerated geomagnetic‐equator motion after 1999, the afternoon enhanced trend is suppressed, whereas the morning decreased trend is strengthened for the full‐period (1967–2015) data set. The semidiurnal‐like pattern in the EEJ long‐term trend is possibly related to the weakened migrating semidiurnal tide (SW2) caused by the enhanced greenhouse gases as reported in previous studies. Our results disentangle the influences of greenhouse gas and geomagnetic secular variation on equatorial ionospheric electrodynamics, and have potential implications for ionospheric climate and weather.