Yanjing Theological Seminary was jointly established in 1986 by seven provincial or municipal CC&TSPMs (in Beijing, Tianjin, Hebei, Shanxi, Shaanxi, Gansu, Qinghai), as well as the CC&TSPMs in Inner Mongolia Autonomous Region, Ningxia Autonomous Region, and Xinjiang Autonomous Region. It is one of the five regional theological seminaries and the only Christian seminary located in Beijing.

Northeast Theological Seminary has a history over one hundred years. In 1894, Dongguan Presbyterian Church established an advanced theological course based upon a pastor training class, with the purpose of cultivating local clergy. That was the predecessor of Northeast Theological Seminary. The seminary was officially set up in 1898 (in Shenyang, Liaoning), and Rev. Dr. John Ross (a Scottish Presbyterian missionary, 1842-1915) served as the first president.