Earth’s interannual climate variability is dominated by El Niño/Southern Oscillation (ENSO). Palaeoclimate records indicate a lower ENSO variance during the middle Holocene compared with today1, 2, 3, 4, 5, 6; however, model simulations have not reproduced the full magnitude of the changes7, 8, 9, 10, and whether external forcing drives large intrinsic ENSO variability11 is therefore a matter of considerable debate. Here we present a 175-year-long, monthly resolved oxygen isotope record, obtained from a Porites coral microatoll located on Kiritimati (Christmas) Island, in the NINO3.4 region of the central equatorial Pacific. Our quantitative record of ENSO variability about 4,300 years ago shows that ENSO variance was persistently reduced by 79%, compared with today, and it exhibits a dominant annual cycle. Season-specific analysis shows that El Niño events were damped during their September–November growth phase, and delayed relative to the climatological year. We suggest that the higher boreal summer insolation at the time strengthened the tropical Pacific zonal winds as well as the gradients in sea surface temperature, and thereby led to an enhanced annual cycle and suppressed ENSO. As the weak ENSO is subject to interdecadal amplitude modulation, we conclude that amplitude modulation is likely to remain robust under altered climates. Our findings show that ENSO is capable of responding to external forcing.