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The Saudi Ministry of Health (MOH) established a National School-Based Screening Program (NSBSP) for health screening of schoolchildren. Students from specific grades were systematically screened for several health problems, including obesity, visual and auditory problems, dental cavities, scoliosis, and attention-deficit/hyperactivity disorder (ADHD). This cross-sectional study aimed to determine the prevalence of these health problems among primary school students based on secondary data obtained from the NSBSP. We included 444,259 screened school children from the first and fourth grades of 50% of the selected schools (both private and public) across the Kingdom of Saudi Arabia (KSA) during the academic year 2018–2019. Among them, the most prevalent health problems identified were dental cavities (38.7%), eye refractory errors (10.9%), and overweight and obesity (10.5%); the less prevalent problems included ADHD (2.81%), auditory problems (0.6%), and scoliosis (0.48%). A greater prevalence of most health problems was observed in girls more than boys. The NSBSP successfully aided the detection of health conditions with high and low prevalence among primary school students in the KSA, and thus, the identification of health problems of specific concern. Implementation of effective school health services for the prevention, early detection, diagnosis, and treatment of these health problems are imperative.