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Introduction People in the Gaza Strip have been denied food and medical care through war and displacement since October 2023, introducing the risk of famine in the region. We sought to estimate the proportion of children assessed in nutritional centres with moderate acute malnutrition (MAM) and severe acute malnutrition (SAM) in the Gaza Strip during this war.Methods We conducted a cross-sectional analysis of nutritional assessments for children up to 5 years old in the Gaza Strip, Palestine, from May 2024 to November 2024. We used de-identified data from humanitarian relief clinics to determine the proportion of MAM and SAM. We defined SAM as weight-for-length Z score <−3. For children above 6 months, we additionally used mid-upper arm circumference (MUAC) <11.5 cm to identify SAM. We defined MAM as weight-for-height Z-score between –2 and −3, or MUAC 11.5–12.4 cm. We used logistic regression to determine factors associated with acute malnutrition.Results Of 22 901 children (49.6% girls; 12.0% in North Gaza), there were 2042 (8.92%, 95% CI 8.56% to 9.28%) children diagnosed with SAM or MAM during the study period. SAM was higher in North Gaza/Gaza City than in South/Middle Gaza (15.7% vs 0.4%, p<0.001). In North Gaza/ Gaza City, SAM was associated with having a deceased father (adjusted OR 1.97, 95% CI 1.24 to 3.06) and in children <6 months (adjusted OR 1.86, 95% CI 1.15 to 2.96). The prevalence of SAM decreased in North Gaza/Gaza City during this study period.Conclusion A high proportion of children under 5 years old had evidence of SAM or MAM, particularly in North Gaza and Gaza City, which has been subjected to more intense bombings and restrictions in aid. Cessation of hostilities and resumption of humanitarian aid relief is urgently needed for children in Gaza.