This study investigates the El Niño‐Southern Oscillation (ENSO )‐related seasonal variations in precipitation extremes based on the observed daily precipitation dataset of 23 meteorological stations in Malaysia, spanning a period of 46 years from 1966 to 2011. The extreme indices were a subset of the Expert Team for Climate Change Detection and Indices (ETCCDI ) that covers the duration, frequency and intensity aspects of precipitation extremes. Seasonal composites of ‘El Niño minus neutral’ and ‘La Niña minus neutral’ years of these indices were computed based on El Niño and La Niña occurrences during the period. The results showed that the ENSO ‐related variations in precipitation extremes were generally coherent with the variations in total precipitation. Generally, dry (wet) precipitation extremes tended to enhance during El Niño (La Niña); however, this was dependent on season and location. The El Niño and La Niña influences on precipitation extremes were not entirely linear. While the impacts of El Niño and La Niña were generally opposite for most locations and seasons, there were cases where both exerted in‐phase influences. The impacts were also dependent on the intensity of the event itself. While the El Niño impacts were generally coherent across different intensities, La Niña can have entirely different impacts among different categories. During December–January–February (DJF ), strong (moderate) La Niña caused a significant decrease (increase) in wet precipitation extremes over the Peninsular Malaysia. This was related to the broadening (narrowing and westward displacement) of the anomalous cyclonic circulation over the western north Pacific during strong (moderate) La Niña. Hence, the likelihood for widespread flooding over the east coast of the Peninsular Malaysia during DJF increases during moderate but not during strong La Niña events.