An accelerated epidemiological transition, economic development and urbanization have brought rapid reductions but a potential disparity in infectious diseases burdens in-school and out-of-school children, adolescents, and youths in China. This paper assesses the disparity in spectrum of infectious diseases between two groups, and described disparity's variation by age, year and province, and determined the priority diseases. A total of 7,912,274 new incident cases (6,159,021 in school and 1,753,253 out of school) aged 6-21 years across 43 notifiable infectious diseases have been collected based on China's Notifiable Infectious Disease Surveillance System from 2013 to 2021. All infectious diseases are categorized into seven categories: vaccine preventable, bacteria, gastrointestinal and enterovirus, sexually transmitted and bloodborne, vectorborne, zoonotic, and quarantinable diseases. We used the index of incidence rate ratio (IRR) of by specific disease, category, year, and age to assess the disparity between those out-of-school and in-school, and determine their separate priority diseases. From 2013 to 2021, a small disparity of notifiable infectious diseases existed with higher average yearly incidence for out-of-school children, adolescents, and youth than that in-school (327.601 v.s. 319.677 per 100,000, IRR=1.025, 95%CI: 1.023-1.027, standardized IRR=1.169, 95%CI: 1.155-1.183), and it gradually narrowed by surveillance years with IRR from 1.351 in 2013 to 1.015 in 2021 due to large decreased disparity in compulsory education stage group. Such disparity was mainly driven by sexually transmitted and bloodborne diseases, bacteria diseases, vectorborne diseases, quarantinable diseases and zoonotic diseases. However, vaccine preventable diseases, gastrointestinal and enterovirus diseases showed higher incidence of infectious diseases for those in-school than that out-of-school, particularly for seasonal influenza, mumps and hand-foot-and-mouth disease. Meanwhile, such disparity is obvious in most of ages and in eastern and coastal regions of China, and the narrowing trend is attributed to six categories diseases, except for sexually transmitted and bloodborne diseases with gradually widened disparity between two groups with surveillance years with IRR from 22.939 in 2013 to 23.291 in 2021 due to large disparity for those who have completed compulsory education. A huge achievement has been achieved in reducing the burden and disparity of infectious diseases between out-of-school and in-school children, adolescents, and youths in China, particularly for the compulsory education stage population. The priorities for the coming decades will be to extend successful strategies to a broad scope and promote education, particularly for the investment of social health resources and the improvement of personal health literacy in the non-compulsory education stage. This should involve extending the years of compulsory school, improving sex health education, strengthening monitoring, expanding immunization programs coverage and prioritizing the prevention and control of sexually transmitted diseases and tuberculosis among out-of-school population. National Natural Science Foundation of China and Beijing Natural Science Foundation.