Seasonal rainfall in the Philippines is known to be modulated by the El Niño Southern Oscillation (ENSO) phenomenon, with ENSO warm (cold) events frequently contributing to drought (excessive rainfall) in many areas. Here, using rainfall data from 40 observing stations across the Philippines, it is shown that the seasonal rainfall response to ENSO reverses sign between boreal summer (July–September) and fall (October–December) for both El Niño and La Niña. Above-median, boreal summer rainfall is observed at several stations in the north-central Philippines during El Niño before anomalously dry conditions become manifest the subsequent fall. Conversely, during La Niña below-median summer rainfall occurs at several stations before the onset of anomalously wet conditions in fall. The results are shown to be not simply a consequence of ENSO transitions during boreal spring, but are associated with changes in the large scale monsoon system during the life cycle of ENSO events.