Independent of the possible sources (solar activity, geomagnetic activity, greenhouse effect, etc.) of a global change in the upper atmosphere, it is the sign of a long-term trend of temperature that might reveal the cause of a global change. Long-term change of temperature in the F region of the ionosphere has been studied and is assumed to be expressed in terms of thickness of the bottomside F2 layer characterized by the difference between height of the maximum electron density of the F2 layer hmF2 and altitude of the lower boundary of the F region represented by h′F. Using the difference of two ionospheric parameters has the advantage that it reduces the effect of changes resulting from alteration of equipment and scaling personnel. In this study, in summer only night values of the difference hmF2−h′F and in winter both day and night values have been taken into account considering that h′F might indicate the lower boundary of the F region in these periods. The study of the behaviour of hmF2−h′F taking separately the stations and determining yearly the mean measure (trend) of the variation of hmF2−h′F with solar and geomagnetic activities found that this difference increases significantly with enhanced solar activity, but trends of the solar activity effect exerted on this difference themselves do not practically change with increasing sunspot number. Further, hmF2−h′F decreases only insignificantly with growing geomagnetic activity. Trends of the geomagnetic activity effect related to hmF2−h′F change only insignificantly with increasing Ap; however, trends of the geomagnetic activity effect decreased with increasing latitude. As a result of this investigation it has been found that hmF2−h′F regarded as thickness of the bottomside F2 layer shows an effect of the change of solar activity during the last three solar cycles, indicating temperature change in the upper atmosphere to be expected on the basis of changing solar activity. Furthermore, though a long-term variation of solar activity considering only years around solar activity minima is relatively small, the difference hmF2−h′F indicates a trend opposing the change of solar activity; that is, it decreases slightly during the first three 20, 21, 22 solar cycle minima (1964–1986), but decreases more abruptly according to the change of solar activity towards the minimum of solar cycle 23 (1986–1996), thus also indicating variation of temperature in the F region. However, this variation cannot be explained by the change of solar and geomagnetic activities alone, but assumes some other source (e.g. greenhouse gases) too.