During active geomagnetic conditions, a large amount of energy is deposited in the polar atmosphere in the form of particle precipitation that leads to Joule heating creating circulation of intense currents in the auroral region. It can affect the existing background pressure fluctuations in the stratospheric and tropospheric heights, leading to anomalous changes in the vertical temperature (T), zonal (u) and meridional (v) wind. In this study, we demonstrate the effect of active geomagnetic conditions on these atmospheric variables in different longitudinal regions. The investigation involves daily, monthly and seasonal variation of active geomagnetic conditions. Active geomagnetic conditions are selected using geomagnetic activity indices like auroral activity index |AL|>1000 nT, Disturbed Storm time index Dst < -150 and polar cap index PC > 5. Events are identified during November to March for 1990 to 2020 period. Among them 99 active geomagnetic conditions occurred in the month of March which are considered for further investigation. Composite analysis of T, u and v reflects that the temperature shows an increase in the entire atmospheric column; the anomalies in u (u′) and v (v′) show a regional dependence and strengthen in their amplitudes. It is seen from the monthly investigation of March that the Western Pacific, Canadian and East Pacific sectors respond to the active geomagnetic conditions at upper atmospheric pressure levels (approximately 40–70 km altitude) in the polar region. This is indicative of a vertical translation of energy to lower atmosphere during active geomagnetic conditions.