Aims. Floods badly impact the food and nutrition security in developing countries. The role of the government and the impact of floods on the underweight status of children in the affected areas is not clear. We aimed to find the determinants of underweight in flood-affected areas of Khyber Pakhtunkhwa, Pakistan. Methods. We used a multistage sampling technique and selected 656 households during in the flood-affected areas of Pakistan. Data were collected in the three most affected districts. A validated questionnaire was used to find socioeconomic and demographic information, hygiene, and sanitation information. We used logistic regression to find the determinants of underweight, controlling for confounders. Results. The prevalence of global malnutrition based on underweight was 25.2%. The prevalence of underweight was higher in young age mothers (40.6%), younger age children (71.4%), large family size (28.4%), joint family (27%), and no toilet facility (28.9%). District Nowshera was at high risk of underweight based undernutrition, followed by district Charsadda compared to children belonging to Dera Ismail Khan. The significant risk factor that causes underweight was child lower age (p < 0.01), young age of mothers (p < 0.01), children access to unimproved water sources (p < 0.01), and location (districts) due to environmental and constant flood consequences (p < 0.01). Conclusion. In conclusion, risk factors of underweight should be appropriately targeted in the flood-hit areas of Pakistan. Governments should preallocate budgetary resources and enhance the emergency preparedness levels to facilitate the communities with flooding incidents and their aftermath in the shape of child underweight-based malnutrition.