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The present study investigated the variability in Equatorial electrojet (EEJ) and Counter electrojet (CEJ) extracted at the Indian equatorial station Tirunelveli (TIR) using low‐latitude geomagnetic conjugate sites, Hyderabad (HYB) and GAN Island (GAN) from the northern and southern hemispheres respectively over a period of 5 years. A significant difference in the amplitudes, of more than 10 nT for 43% of the days, is observed when the TIR‐HYB pair and the TIR‐GAN pair are used. Occurrence of CEJs are 60% more when the TIR‐GAN pair is considered. A correlation coefficient of 0.9 is obtained between the monthly mean peaks of diurnal variations in H between TIR and GAN; this correlation coefficient is 0.66 between TIR and HYB. The correlation coefficients from the first principal components of H, at these sites show variability with seasons; the correlation observed between TIR and GAN is higher than that between TIR‐HYB for all seasons except northern winter. This indicates the coupling of EEJ with Sq of both northern or southern hemispheres with varying extents. The present study highlights that the extraction of EEJ/CEJ using Sq from only one hemisphere will lead to biased estimates; even a small difference in the seasonal pattern of ∆H at equatorial and low latitude sites can result in the over/under‐estimation of EEJ and hence CEJ. Plain Language Summary: EEJ and CEJ extracted using Sq from only one hemisphere may lead to over/under‐estimation of EEJ and CEJ, as the Sq at EEJ site may be coupling with either northern or southern Sq. We report large variations in EEJ and CEJ at TIR when extracted using Sq at low latitude of northern hemisphere, HYB and of southern hemisphere GAN. Observations from TIR, HYB and GAN shows diurnal variations in H at TIR(EEJ site) is more similar to southern Sq at GAN than northern Sq at HYB. An over‐estimated EEJ is observed while using TIR‐HYB for September month, which resulted in equinox asymmetry of EEJ, that is, EEJ is stronger in SEP than in MAR. These observations do not exist when GAN is used to derive EEJ at TIR. Many more CEJs are observed for TIR‐GAN pair than TIR‐HYB. Thus the conventional way EEJ is derived using Sq from any one of the hemispheres, is not accurate. Key Points: Equatorial electrojet (EEJ) is coupled to Sq of both hemispheres and the nature of coupling varies with seasonsEEJ/Counter electrojet patterns considering influence of Sq of both hemispheres, instead of only northern hemisphere exhibit significant differences [ABSTRACT FROM AUTHOR]