To compare the accuracy of three different screening tools, namely, the Paediatric Yorkhill Malnutrition Score (PYMS), Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP), and Screening Tool for Risk on Nutritional Status and Growth (STRONGKIDS), in assessing malnutrition risk in hospitalised children. A cross-sectional study was conducted on 300 children aged 6 months to 15 years at Alexandria University Children's Hospital, Egypt. The sensitivity and specificity of each tool were calculated to detect acute and chronic malnutrition, and an agreement test was conducted between the nutritional screening tools. The patients were classified into different nutritional risk groups, and their classification was compared with anthropometric measures and clinical variables, such as the length of hospital stay (LOS). The prevalence of stunting and wasting on admission was found to be 3% and 6.6%, respectively. Children categorised as high-risk on admission had a longer LOS than those at low risk. The agreement test between the STAMP score and STRONGKIDS score on admission showed the most significant agreement, and STRONGKIDS had the best accuracy in detecting acute and chronic malnutrition. The comparison of the three screening tools revealed that STRONGKIDS exhibited the best accuracy in detecting acute and chronic malnutrition.