This study investigates the response of the equatorial ionosphere to the tropospheric Madden‐Jullian Oscillation (MJO) using the Whole Atmosphere Community Climate Model‐eXtended (WACCM‐X). Main results indicate that the intraseasonal variability of ionospheric vertical plasma drifts (Viz) is generally strong around boreal winters and exhibits significant eastward‐propagating signals. Composite analysis showed that, during the December‐January‐February‐March (DJFM) season, Viz was generally negative when the MJO was active over the Maritime Continent (Phase 5) and positive when the MJO was active over the Indian Ocean (Phase 2). The magnitude of MJO impact on Viz achieves ∼1.2 m/s, representing roughly 10% of the seasonal mean. The eastward‐propagating wavenumber‐4 is apparently strong during MJO phases 5 and 1–2, which is examined to be associated with non‐migrating tides below. Term analysis revealed the importance of zonal winds on driving the Viz responses. This study emphasizes the importance of tropospheric sources that affect the geospace environment.