It is still unclear how El Niño Southern Oscillation (ENSO), the leading mode of global-scale interannual climate variability, will respond to global warming. The last deglaciation offers natural experimental conditions to observe the behavior of ENSO in a period of abrupt warming and sea level rise. Here we present a record of ENSO-related interannual variability of river discharge in Peru during the last deglaciation (17.3-13 kyr) and the Late Holocene (2.7-1.3 kyr), based on high-resolution records of Titanium concentration in marine sediments from the Peruvian margin (Callao, 12°S and Pisco 14°S). We find that the amplitude of ENSO events was 16 to 100 % larger during the last deglaciation compared to the Late Holocene, which supports the hypothesis that ENSO in the EP is strengthened by ice sheet meltwater discharge. A possible strengthening of ENSO in response to future ice sheet melting should be considered.