The Weather Research and Forecasting (WRF) model is used to dynamically downscale 27 years of the Climate Forecast System Reanalysis (CFSR) in a tropical belt configuration at 36 km horizontal grid spacing. WRF is found to give a good rainfall climatology as observed by the Tropical Rainfall Measuring Mission (TRMM) and to reproduce well the large-scale circulation and surface radiation fluxes. The impact of conventional and Modoki-type El Niño–Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD) are confirmed by linear regression. Madden–Julian Oscillation (MJO) and Boreal Summer Intra-seasonal Oscillation (BSISO) are also well-simulated. The WRF simulation shows that conventional El Niño increases (La Niña decreases) the MJO amplitude in the boreal summer while Modoki-type ENSO and IOD impacts are MJO-phase dependent. While WRF is found to perform well on seasonal to sub-seasonal timescales, it does not capture well the diurnal cycle of precipitation over the Maritime Continent. For the investigation of multi-scale interactions through the local diurnal cycle, TRMM data is used instead. In the Maritime Continent, moderate El Niño and La Niña causes anti-symmetric enhancement/reduction of the MJO’s influence on the diurnal cycle amplitudes with little change in the diurnal phase. Non-linear impacts on the diurnal amplitude with changes in diurnal phase manifest during strong ENSO. Given that the simulation does not employ data assimilation, this modified version of WRF submitted to the model developers is a suitable downscaling tool of CFSR for sub-seasonal to seasonal tropical atmospheric research.