The occurrence patterns of ionospheric irregularities during quiet geomagnetic conditions over the African low latitude region were analysed. GNSS-derived Total Electron Content of the ionosphere data during the period 2001–2012 were used. The data were obtained from Libreville, Gabon (0.35°N, 9.68°E, geographic, 8.05°S, magnetic), Mbarara, Uganda (0.60°S, 30.74°E, geographic, 10.22°S, magnetic), and Malindi, Kenya (2.99°S, 40.19°E, geographic, 12.42°S, magnetic). The rate of change of total electron content index greater than 0.5TECU/Min were considered as severe ionospheric irregularities. For most of the time, the strength of ionospheric irregularities in March equinox were greater than those during September equinox over East Africa and an opposite observation was made over West Africa. These asymmetries might be due to the direction of the meridional winds during equinoxes over the different stations. Severity of ionospheric irregularity reduced from west towards the east. This might have been related to the decreasing geomagnetic field strength from east towards the west. This is the first study that reveals the equinoctial asymmetry is different in the West and East African sectors. Moreover, the importance of this study lies in the fact that it has used extensive data to examine the isolated and un-explained earlier observations of equinoctial asymmetry and longitudinal variation of ionospheric irregularities over the African low latitude region.