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Both neonatal hypothermia and hyperthermia represent important risk factors for neonatal mortality, but information on mortality risk across a full range of neonatal temperatures is lacking in low-resource settings. We evaluated the association between neonatal mortality and a full range of admission temperatures in a low-resource setting. This retrospective observational study was conducted at Beira Central Hospital, Mozambique. The relationship between admission temperature and mortality was evaluated using multivariable analyses with temperature modeled as non-linear term. Among 2098 neonates admitted to the Special Care Unit between January–December 2017, admission temperature was available in 1344 neonates (64%) who were included in the analysis. A non-linear association between mortality rate and temperature was identified. Mortality rate decreased from 84% at 32 °C to 64% at 34.6 °C (− 8% per °C), to 41% at 36 °C (− 16% per °C), to 26% to 36.6 °C (− 25% per °C) and to 22% at 38.3 °C (− 2% per °C), then increased to 40% at 41 °C (+ 7% per °C). Mortality rate was estimated to be at minimum at admission temperature of 37.5 °C. In conclusions, the non-linear relationship highlighted different mortality risks across a full range of neonatal temperatures in a low-resource setting. Admission temperature was not recorded in one third of neonates.