In this extensive study examining the health of 7184 school children aged 3 to 12 in 27 Lebanese schools, screenings involved medical evaluation and interviews, complemented by phone interviews with 3880 parents. Notably, one in two students received a medical referral, revealing prevalent issues such as dental cavities (33%), under-vaccination (25%), undetected vision problems (13%), abnormal growth (6%), underweight (27%), and overweight (33%). Additional concerns encompassed abnormal vital signs (3%), abuse signs (0.6%), infectious skin lesions (1.6%), scoliosis (1.7%), abnormal auscultation (heart 1.1%, lungs 1.2%), ear problems (3.3%), precocious puberty (0.7%), and neurologic signs (0.6%). Mental health challenges affected 20–25% of students. Public schools and Beirut exhibited higher referral rates, with girls, older children, overweight students, those lacking regular pediatrician visits, and children of self-employed or less educated parents facing elevated referral rates. In contrast, children of healthcare workers experienced fewer referrals. Against this backdrop, the study emphasizes the imperative for targeted health initiatives, particularly in marginalized areas and for socioeconomically disadvantaged students. Priority areas include dental care, weight issues, mental health, vaccination compliance, and addressing vision problems to enhance learning outcomes.