Southeast Asia is a region dominated by high‐impact weather, but numerical weather prediction here is a challenge owing to the complex orography and interactions between small‐ and large‐scale phenomena. Localised mesoscale convective systems (MCSs) can produce intense precipitation. Here, we track MCSs over a 5‐year period in Himawari satellite data, characterise the distribution of MCSs in the region, and investigate how they are modulated by the Madden–Julian oscillation (MJO) and equatorial waves. Between 10°S and 10°N in southeast Asia, MCSs account for 45–70% of the precipitation during boreal extended winter (November–April). Over most of the region, the fractional MCS contribution to rainfall is higher than average on days with extreme rainfall (>55%). Long‐lived (>12 hr) MCSs contribute disproportionately, providing 85% of the rainfall despite comprising only 34% of all MCSs. Variability in MCS rainfall accounts for >50% of the total rainfall variability during an MJO cycle, mostly due to larger numbers of MCSs in convectively active MJO phases. Variations in MCS size and mean rain rate due to shifts in the stratiform proportion provide compensating effects. In the west of the region, a shift to faster moving MCSs in active MJO phases and slower moving MCSs in inactive phases resulted in fast‐moving MCSs having the greatest impact on the MJO‐associated variability. Variability is larger in the west than in the east. Equatorial Kelvin waves modulate MCS rainfall, with MCSs accounting for 20–50% of local rainfall anomalies. This variability is again enhanced in the west. By contrast, rainfall anomalies due to westward‐propagating mixed Rossby–gravity waves and Rossby‐1 waves are dominated by tropical‐cyclone‐related rainfall. Skill at local scales may be extracted from forecasts of subseasonal drivers such as the MJO and Kelvin waves, by understanding how these modulate the number and characteristics of MCSs.