Objective: To establish a risk assessment system for the prevention and control of infectious diseases in primary and secondary schools in Tianjin and reduce the risk of infectious disease prevention and control through risk assessment and control. Methods: Based on the failure modes and effect analysis method, a quantitative risk assessment of infectious disease prevention and control in 45 primary and secondary schools in Tianjin was carried out. Risk based supervisory process was assessed, while control effect was evaluated for contined improvement in the prevention and control of infectious diseases in the primary and secondary schools. Results: The top three risk aspects found in the infectious disease prevention and control system in primary and secondary schools in Tianjin included failure to provide sanitation professionals (82.22%) in accordance with regulations, no hand sanitizer or disinfectant (35.56%) in wash basins, and drinking water related products without approval (28.89%). The results of the risk assessment indicated that the three risk aspects with the highest risk priority number (RPN) included failure to provide health professionals( n = 144), no morning and afternoon inspection arrangement( n =126), and low quality of morning and afternoon inspections( n =126). After optimizing the supervision measures for the risk aspects with a detectable degree≥7 points, a quantitative risk assessment was carried out again, the RPN values of all risk points fell below 125, indicating reasonable control effect. Conclusion Based on the failure mode and effect analysis method, the establishment of a risk assessment system for the prevention and control of infectious diseases in primary and secondary schools and regular risk assessments can timely detect risk aspects in the infectious disease prevention and control, to promote effective prevention of infectious diseases in schools.