Numerical simulation has been used to examine the effect of changes in solar activity (SA) in the thermosphere on amplitudes of long-period planetary waves (PW) for the winter period in the Northern Hemisphere. The model of the middle and upper atmosphere (MUAM) is used. It allows simulations of general atmospheric circulation at altitudes 0–300 km. In order to reproduce SA changes, different values of the solar radio flux at a wavelength of 10.7 cm at an altitude of more than 100 km are set in the MUAM radiation block. To take into account the effect of charged particles in the ionosphere on the neutral gas dynamics, ionospheric conductivities for different SA levels are included in MUAM. To improve the statistical reliability of the results, two ensembles of model simulations consisting of 16 runs corresponding to the minimum and maximum SA have been obtained. The statistical confidence of average differences in PW amplitudes between high and low SA has been calculated. The results are shown to be reliable in almost the entire altitude range 0–300 km. Results of the simulations have shown for the first time that statistically significant differences in amplitudes of long-period PWs can reach 10–15 % in the middle atmosphere of the Northern Hemisphere, depending on the zonal wave number. At the same time, reflection of PWs at altitudes of lower thermosphere has a significant effect on the PW structure in the middle atmosphere.