China Education Research Office of the Central Research Academy, which was founded by the Communist Party of China in 1941 in Yan'an, Shaanxi province, was regarded as the predecessor of CNAES. The mission of the Office at that time was to study and solve the theoretical and practical problems of education in the Ear of New Democracy. Li Weihan, then deputy Director-general of the Publicity Department of the CPC Central Committee served as the director of the Office.

In June 1956, Ministry of Education of the People’s Republic of China made the decision to establish the Institute of Educational Sciences based on the personnel from the Editorial Office of People's Education Press and Educational Books Editorial Office.

In January 1957, the China National Institute of Educational Research was officially established under the authorization of the State Council.

In 1978, after the Cultural Revolution, the China National Institute of Educational Research was restored and rebuilt under the authorization of the State Council.

Since 1995, according to the unified deployment of the Ministry of Education, institutional adjustments have been made several times in succession.

In August 2011, the institute was renamed as the National Institute of Education Sciences (NIES). A solemn founding ceremony was held in the Great Hall of the People in Beijing in November.

In 2021, NIES merged with National Centre for Education Development Research (NCEDR, founded in 1986) to form the current China National Academy of Educational Sciences (CNAES).