Several studies have examined ionospheric variation associated with meteorites, meteoroids, or meteors based on Global Satellite Navigation System total electron content observations. However, there have been few quantitative studies of the D‐region of the ionosphere (60–90 km), which is associated with meteoroids. We investigated variation in the D‐region during the passage of a meteoroid over northeastern Hokkaido, Japan, at 11:55:55 UT on 18 October 2018, using very low‐frequency (VLF, 3–30 kHz) and low‐frequency (LF, 30–300 kHz) signals observed by three transmitters [JJY (40 kHz), JJY (60 kHz), and JJI (22.2 kHz)], at Rikubetsu, Japan. Periodic variation of 100–200 s was observed in the VLF and LF amplitudes upon arrival of the acoustic wave. The vertical seismic velocity of Hi‐net and F‐net data also showed acoustic waves. Although the main period of the acoustic wave was 0.1–0.5 s in the seismic data, a longer period component (100–200 s) remained during propagation up to the D‐region ionosphere. The estimated velocity of the acoustic waves was ∼340 m/s on the ground according to the Hi‐net seismic data. The acoustic wave originated near the endpoint (25 km altitude) of the meteoroid trajectory. Based on the observed propagation time of the acoustic waves and ray tracing results, the acoustic waves propagated obliquely from near the endpoint of the meteoroid trajectory up to a D‐region height (about ∼90 km altitude), south of the Rikubetsu receiver.