Pup mortality and the timing of birth of South American sea lions Otaria flavescens were investigated to determine the possible relationship between fluctuations in prey availability in the Peruvian upwelling ecosystem and current and future reproductive success of sea lions during six consecutive breeding seasons. Our study from 1997 to 2002 encompassed the strongest El Niño on record and one La Niña event. Pup mortality ranged from 13% before El Niño to 100% during El Niño, and was negatively correlated with prey availability. Abortions were also more frequent when prey availability was low. However, pup mortality remained high following El Niño due to the punctuated short-term effects it had on population dynamics and subsequent maternal behaviour. Births occurred later in the season after years of low food availability and earlier following years of high food availability. The peak of pupping occurred around the peak of mortality in all years, and may have been the product of intensive competition between bulls at the peak of the breeding season. The stronger and more frequent El Niños that appear to be occurring along the Peruvian coast may produce significant stochastic changes in future births and pup mortality, which may place the vulnerable South American sea lion population in Peru at greater risk.