Background Hospitalized children present higher rates of undernutrition. Malnutrition can lead to a more complex hospitalization process with an increased length of stay and higher costs. Our aim was to analyze nutrition risk in hospitalized children and its relationship with clinical outcomes in a tertiary level hospital. Methods This is a single institution prospective observational study. The research involved 282 consecutive children admitted along 3 months. Anthropometric measurements and nutrition risk by means of the Screening Tool for Risk on Nutritional Status and Growth (STRONGkids) tool were performed at admission. The incidence of infectious complications, length of hospital stay, weight loss, hospital expenses, and need of nutrition support were recorded. Results The percentage of children with high, moderate, and low nutrition risk was 12.8%, 45%, and 42%, respectively. The prevalence of acute and chronic malnutrition was 13.7% and 7.4%. STRONGkids score correlated with clinical outcomes: longer stay, higher hospital expenses, and need of nutrition support were observed in children with high nutrition risk scores compared with the other groups (P < 0.001). The overall incidence of infectious complications was low (3.5%); a higher STRONGkids score did not predict a higher rate. Conclusion Hospitalized children exposed to high nutrition risk have poorer clinical outcomes: longer stay, higher hospital expenses, and need of nutrition support. More studies are required to assess if applying STRONGkids and starting a nutrition intervention would result in lower costs and a shorter length of stay.