Background Early detection of children at risk of developing malnutrition during hospitalization prevents the development of complications. This study aims to determine the malnutrition risk of pediatric inpatients by using three different nutrition screening tools and to evaluate the reliability/sensitivity of the screening tools. Methods This cross‐sectional study included 176 children who were 1–16 years of age and were admitted to the pediatrics service of a second‐line hospital. Body weight and height were used to evaluate the nutrition status of children. Age‐ and sex‐specific z‐score values for height for age (HFA), weight for age (WFA), and body mass index for age (BFA) were indicators of malnutrition. The Screening Tool for Risk of Impaired Nutritional Status and Growth (STRONGkids), Pediatric Yorkhill Malnutrition Score (PYMS), and Pediatric Nutrition Screening Tool (PNST) were used under the responsibility of pediatricians and dietitians to evaluate the risk of malnutrition in children. Results At admission, according to the HFA, BFA, and WFA SD scores (SDSs), the incidence of malnutrition in children was 8.5%, 14.8%, and 6.3%, respectively. Three screening tools determined that WFA SDSs were significantly higher in children without malnutrition risk than in those at risk of malnutrition (P < 0.05). PYMS revealed a relatively higher sensitivity of 90.9% and 84.6% for WFA and BFA, respectively, and PNST revealed a relatively higher sensitivity of 88.9% for HFA. Conclusions PYMS and PNST are suitable for use in malnutrition risk assessment in pediatric inpatients because of the screening tools’ high sensitivity.