AbstractThe current study is a first‐of‐its‐kind in that it compares the Total Electron Content (TEC) of the solar cycle from the Global Positioning System (GPS) and Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model (TIE‐GCM) over the geomagnetically conjugate low‐latitude stations with the particular scenario of lower atmospheric conditions over land‐ and sea‐locked locations. For this, TEC data for the period 2009–2017 is used from northern hemispheric stations Varanasi (25.31°N; 82.97°E) and LHAZ (29.65°N; 91.10°E) and southern hemispheric stations DGAR (7.27°S; 72.37°E) and COCO Island (12.18°S; 96.83°E). The solar cycle variation in TEC is identified by two distinct maxima and hysteresis between the ascending and descending phases. The solar cycle trends are modulated by the equatorial ionization anomaly as well as longitudinal biases. The Lomb‐Scargle periodogram shows that the improved TIE‐GCM version 2.0, which incorporates variable eddy diffusion to provide an accurate simulation of seasonal variability, is largely successful in simulating semi‐annual and annual oscillations but still needs to resolve the seasonal anomaly feature, particularly in the case of southern low latitude stations. Terannual (120‐day) and 1.4‐year (500‐day) periodicities in the TEC time series are observed only at EIA region stations, not at off‐crest location LHAZ, and are most likely caused by E x B drift. The wavelet coherence analysis reveals that the Quasi Biannual Oscillations (QBO) in the TEC time series (597‐, 773‐, and 930‐day) have a strong physical affinity with the QBO oscillation of F10.7 flux. Results indicate that both solar activity and equatorial electrodynamics significantly influence the QBO oscillation in the TEC.