In mid- and low-latitude ionospheric F-region on the dayside, magnetic field and electron density (Ne) fluctuations with amplitude smaller than a few nT and 1–2% of Ne, respectively, are commonly observed. Their spatial scale along satellite orbit is around 70–250 km. It is presumed that they are generated by the waves propagated from lower atmosphere. However, the mode of waves (acoustic wave or internal gravity wave) and their source are not yet clear. Among the possible sources, cumulus convection and/or associated rainfall are considered to be the strong candidates for the atmospheric wave generation. We use the rainfall estimated by the hourly Global Satellite Mapping of Precipitation (JAXA/GSMaP) as a proxy of lower atmospheric disturbance as the wave source, and compare the rainfall with the amplitude of magnetic fluctuations (magnetic ripples) and electron density fluctuations observed by the Swarm satellites. The data from April 2014 to July 2020 are used. The global distribution of rainfall estimated by the GSMaP and its seasonal variation have similarities with amplitude distribution of magnetic ripples and electron density fluctuations on the dayside. We calculate the ratio of their magnitude, i.e., amplitude of magnetic ripples or electron density fluctuations in rainfall cases to those in no-rainfall cases. Although the longitudinally averaged ratio is not very large but around 1.1–1.2 in ± 10– ± 50° Apex latitudes, it is clearly larger than 1.0. The ratio increases when the intensity of rainfall (mm/h) increases. These results indicate that a cumulous convection which causes rainfall is one of the main sources of atmospheric waves that produce magnetic ripples and electron density fluctuations commonly observed in the dayside ionosphere. Anticipating acoustic waves as the driver of magnetic ripples and electron density variations, a difference in the generation mechanism of electron density fluctuations from that of magnetic ripples is suggested even if their sources are common.Graphical abstract