Here we present a high-resolution marine sediment record from the El Niño region off the coast of Peru spanning the last 20,000 years. Sea surface temperature, photosynthetic pigments, and a lithic proxy for El Niño flood events on the continent are used as paleo–El Niño–Southern Oscillation proxy data. The onset of stronger El Niño activity in Peru started around 17,000 calibrated years before the present, which is later than modeling experiments show but contemporaneous with the Heinrich event 1. Maximum El Niño activity occurred during the early and late Holocene, especially during the second and third millennium B.P. The recurrence period of very strong El Niño events is 60–80 years. El Niño events were weak before and during the beginning of the Younger Dryas, during the middle of the Holocene, and during medieval times. The strength of El Niño flood events during the last millennium has positive and negative relationships to global and Northern Hemisphere temperature reconstructions.