Background: Global warming is predicted to indirectly result in more undernutrition by threatening crop production. Whether temperature rise could affect undernutrition directly is unknown. We aim to quantify the relationship between short-term heat exposure and risk of hospitalization due to undernutrition in Brazil. Methods and findings: We collected hospitalization and weather data for the hot season (the 4 adjacent hottest months for each city) from 1,814 Brazilian cities during 1 January 2000.31 December 2015. We used a time-stratified case-crossover design to quantify the association between heat exposure and hospitalization due to undernutrition. Region-specific odds ratios (ORs) were used to calculate the attributable fractions (AFs). A total of 238,320 hospitalizations for undernutrition were recorded during the 2000.2015 hot seasons. Every 1°C increase in daily mean temperature was associated with a 2.5% (OR 1.025, 95% CI 1.020.1.030, p < 0.001) increase in hospitalizations for undernutrition across lag 0.7 days. The association was greatest for individuals aged ≥80 years (OR 1.046, 95% CI 1.034.1.059, p < 0.001), 0.4 years (OR 1.039, 95% CI 1.024.1.055, p < 0.001), and 5.19 years (OR 1.042, 95% CI 1.015.1.069, p = 0.002). Assuming a causal relationship, we estimate that 15.6% of undernutrition hospitalizations could be attributed to heat exposure during the study period. The AF grew from 14.1% to 17.5% with a 1.1°C increase in mean temperature from 2000 to 2015. The main limitations of this study are misclassification of different types of undernutrition, lack of individual temperature exposure data, and being unable to adjust for relative humidity. Conclusions: Our study suggests that global warming might directly increase undernutrition morbidity, by a route other than by threatening food security. This short-term effect is increasingly important with global warming. Global strategies addressing the syndemic of climate change and undernutrition should focus not only on food systems, but also on the prevention of heat exposure.