The study presents the results of comparative analysis of features of a short-period (with periods of internal gravity waves) variability of total electron content (TEC) in the ionosphere at middle (Novosibirsk) and high (Norilsk) latitudes over a long period of time (2003–2020). The period analyzed makes it possible to estimate not only diurnal and seasonal variations in the variability, but also its changes within the solar activity cycle. The level of TEC variability is shown to experience pronounced seasonal variations with maxima in winter months. The difference between the level of variability in winter and summer is about two times for Novosibirsk and up to seven times for Norilsk. The variability features a distinct diurnal variation; however, the diurnal dependence at the mid- and high-latitude stations differs significantly. At high latitudes, the level of variability in the winter period strictly depends on solar activity. For the mid-latitude station, there is no clear dependence of variability level on solar activity; in the years of solar maximum, on the contrary, a slight decrease in the variability is observed. In summer, the level of variability at both middle and high latitudes remains practically unchanged and does not depend on solar activity. The main features in the dynamics of variability are shown to be similar at stations located at other longitudes, except for the East American sector. The result obtained suggests that the short-period TEC variability at high latitudes is primarily related to changes in solar activity, but regular variations in the variability at midlatitudes are probably not associated with heliophysical activity. The observed increase in the level of short-period variability in the winter mid-latitude ionosphere is assumed to be related to an increase in wave activity in the stratosphere.