Whole Atmosphere Community Climate Model (WACCM) simulations are used to investigate the migrating and nonmigrating tidal variability in the mesosphere and lower thermosphere (MLT) due to the El Niño–Southern Oscillation (ENSO). The most notable changes occur in the equatorial region during Northern Hemisphere winter in the diurnal migrating tide (DW1), diurnal eastward propagating nonmigrating tides with zonal wavenumbers 2 and 3 (DE2 and DE3), and the semidiurnal westward propagating nonmigrating tide with zonal wavenumber 4 (SW4). The WACCM simulations indicate that the ENSO represents a source of interannual tidal variability of ∼10–30% in the MLT. The tidal changes are attributed to changes in tropical precipitation, altered tidal propagation due to changing zonal mean zonal winds, and changes in planetary wave activity associated with the ENSO. During the El Niño phase of the ENSO the DE2 and DE3 are decreased, and the DW1 and SW4 are enhanced. The opposite response occurs during the La Niña phase of the ENSO; however, the magnitude of the tidal changes due to El Niño and La Niña are different. This is especially notable for the DE2 and DE3 which are enhanced by ∼2 K during La Niña time periods, and only reduced by ∼1 K during El Niño time periods. The results demonstrate that changing sea surface temperatures associated with the ENSO significantly impact the overall dynamics of the MLT. Our results further suggest that the ENSO is a source of significant interannual variability in the low-latitude ionosphere and thermosphere.