The circulation of the stratosphere is strongly influenced by the fluxes of gravity waves propagating from tropospheric sources. In the tropics, these gravity waves are primarily generated by convection. The Madden‐Julian Oscillation (MJO) dominates the intraseasonal variability of this convection. However, the influence of the MJO on the variability of stratospheric gravity waves is largely unknown. Here we examine gravity wave potential energy at 26 km and the upper tropospheric zonal wind anomaly of the MJO at 200 hPa, sorted by the relative phase of the MJO using the Real Multivariate MJO indices. We show that a strong anticorrelation exists between gravity wave potential energy and the MJO eastward wind anomaly. We propose that this correlation is a result of the filtering of upward propagating waves by the MJO winds. The study provides the first observational evidence that the MJO contributes significantly to the global variability of stratospheric gravity waves in the tropics. Key Points MJO signature observed in stratospheric gravity waves Strong anticorrelation between gravity wave energy and eastward zonal wind anomalies Evidence that the MJO modulates stratospheric gravity wave activity through wave filtering