We investigated the variability in the neutral upper atmosphere and ionosphere parameters over East Siberia. The analysis is based on 2008–2014 data set of mesopause temperature (Tm) obtained from spectrometric measurements of the OH emission (834.0 nm, band (6–2)) at the Institute of Solar‐Terrestrial Physics Geophysical Observatory (51.8°N, 103.1°E), and the data of F2 peak electron density (NmF2) from Irkutsk DPS‐4 Digisonde (52.3°N, 104.3°E). The seasonal patterns of the NmF2 and Tm variability in different period ranges were analyzed and compared. The period range included day‐to‐day (periods T > 24 h) and tidal (8 h ≤ T ≤ 24 h) variations as well as variations in the internal gravity wave period range (T < 8 h). The comparison revealed both common features and distinctions in the seasonal patterns of the ionospheric and atmospheric variabilities. The main common feature is that the winter variability exceeds the summer one. In both atmospheric and ionospheric day‐to‐day variability seasonal variations, there are maxima in winter months and an additional maximum around the autumn equinox. The main distinction is that the equinox peaks observed in the seasonal variations of the diurnal atmospheric variability are not seen in the ionospheric seasonal pattern. The physical reasons of the obtained features are discussed. The revealed similarities in the seasonal behaviors may indicate that planetary waves propagating from the lower atmosphere layers have a significant impact on the mesopause temperature regime and ionospheric day‐to‐day variations.