Equatorial Electrojet (EEJ) and Equatorial Ionization Anomaly (EIA) are two distinct ionospheric phenomena which are caused by the horizontal configuration of the geomagnetic field at the equator. On the day side of the earth, these activities are controlled by a common zonal electric field, and their interactions must be researched for a number of scientific reasons. In this study, we used multiple Global Navigation Satellite System (GNSS) stations at Al Wajh, Sola village, Nama, and Sheba in 2012 to investigate the correlations between the instantaneous and integrated equatorial electrojet (EEJ) and the variations of vertical total electron content (vTEC) at the northern crest of EIA in the East Africa and Middle East longitudinal sector. The equinoctial and solstitial months have the highest and lowest values of the monthly mean EEJ and vTEC, respectively, and as a result, both parameters show a semi-annual variability. The monthly mean vTEC also demonstrates equinoctial and solstitial asymmetries, resulting in vTEC values that are higher at the September equinox and the December solstice than at the March equinox and the June solstice, respectively. These asymmetries have been also observed in the composition of [O]/[N2] ratio. On days with strong counter electrojet (CEJ), EEJ peaks are smaller and occur later than on days with weak CEJ. Additionally, when CEJ is high, EIA is suppressed and vTEC exhibits low values at all crest points. In the early hours (10:00–12:00 Lt), Nama and Sheb showed higher correlation coefficient values with significant levels than Alwj and Sola. According to the correlation analysis, the anomaly crest develops at the lower latitude stations between 10:00 and 12:00 Lt and then moves to the higher latitude stations later. Generally, the correlations are higher and more significant in the equinoxes than the solstices. The correlations between integrated EEJ (IEEJ) and vTEC were also found to be strong and significant at the lower latitude stations throughout all seasons. These findings suggest that both the instantaneous and integrated EEJ can be used as a proxy for the eastward zonal equatorial electric field and must be considered in regional and global models of total electron content of equatorial and low latitude ionosphere.