The aim of the study was to investigate Swedish school nurses’ perceptions of schoolchildren’s health. The study is based on two national surveys in which school nurses responded to questions about schoolchildren’s health in 2015 (n = 181) and 2005 (n = 129). A statistical comparison showed that physical and mental health of schoolchildren in high-risk areas was perceived as worse than that of children in low-risk areas. There were no differences regarding the number of spontaneous visits or consulting reasons related to gender in high- and low-risk areas. A national framework for data collection and reporting of schoolchildren’s health may be important for school nurses to demonstrate the need for increased support in, for example, high-risk areas. By paying attention to factors that can affect schoolchildren’s health, school nurses can also direct health promotion to areas where it is needed. Increased cooperation among school health professionals may also prevent illness and improve health.