Stunting is a significant public health problem in low- and middle-income countries. This study assessed the prevalence of stunting and associated risk factors of stunting among preschool and school-going children in flood-affected areas of Pakistan. A cross-sectional study was conducted by visiting 656 households through multi-stage sampling. Respondent's anthropometric measurements, socio-demographic information and sanitation facilities were explored. A logistic regression model was used to determine determinants of stunting, controlling for all possible confounders. The overall prevalence of stunting in children was 40.5%, among children 36.1% boys and 46.3% of girls were stunted. The prevalence of stunting in under-five children was 50.7%. Female children (OR=1.35, 95% CI:0.94-2.0), children aged 13-24 months (OR=6.5, 95% CI: 3.0-13.9), mothers aged 15-24 years (OR=4.4, 95% CI: 2.6-7.2), joint family (OR=2.1, 95% CI: 1.4-3.0) did not have access to improved drinking water (OR=3.3, 95% CI: 1.9-5.9), and the toilet facility (OR=2.8, 95% CI, 1.9-4.3), while the children from district Nowshera (OR=1.7, 95% CI: 0.9-3.2) were significantly (P<0.05) associated in univariate analysis. The regression model revealed that child age, maternal age, family type, quality of water, and toilet facility, were the significant (P<0.05) factors contributing to child stunting in the flood-hit areas. Identification of key factors might be helpful for policymakers in designing comprehensive community-based programs for the reduction of stunting in flood-affected areas. In disasters such as flood, the detrimental consequences of the stunting problem could be even more on children. Evidence-based education and care must be provided to the families in the flood-affected regions to reduce the stunting problem. The determinants of stunting should be targeted by making comprehensive policies regarding proper nutrition, livelihood, clean water, and sanitation facilities in flood-hit regions.