Understanding the controls on stable isotopologues of tropical rainfall is critical for paleoclimatic reconstruction from tropical ice core records. The southern Papua region, Indonesia, has a unique climate regime that allows for the evaluation of the influence of precipitation and convective activity on seasonal rainfall δ18O. The influence of the El Niño–Southern Oscillation (ENSO) on interannual rainfall δ18O variation is also important for paleoclimate reconstruction. Here we present stable isotope analyses of 1332 rain samples collected daily during the period from January 2013 to February 2014 (ENSO‐normal) and December 2014 to September 2015 (El Niño) at various elevation stations (9 to 3945 m above sea level) on the southern slope of the central mountain ranges in Papua. The results suggest an altitude effect with an isotopic lapse rate for δ18O (δD) of −2.4‰/km (−18.2‰/km). The temporal δ18O variability (daily to interannual) is controlled mostly by regional convective activity rather than local/regional precipitation amount. The intraseasonal δ18O variation resembles the Madden‐Julian Oscillation cycle with major δ18O depletion events associated with active (wet) phases. Moisture origins, transport pathways, moisture convergence, and raindrop evaporation appear to have no significant seasonal effects on δ18O, leading to the conclusion that condensation temperature controls δ18O depletion associated with convective activity. Seasonal δ18O variation is likely associated with atmospheric temperature at the mean condensation level as indicated by the altitude of latent heat release in the troposphere. Rainfall δ18O (δD) is generally enriched by 1.6‰–2‰ (11‰–15‰) during El Niño than during ENSO‐normal periods.