Happer went on medical furlough in 1855 and the Second Anglo-Chinese War delayed the Happer's return from furlough until 1859. Followign the war, however, the treaties produced by the war promoted free and unrestricted access to Canton. This led to an upsurge of missionaries into the Canton with increased conversions to Christianity. In the 1860s, Happer founded the First Presbyterian Church, numerous boarding and day schools, and a training school serving preachers, teachers, and colporteurs of Canton. Happer served as pastor of the First Presbyterian Church in Canton, established in 1862. Through establishing multiple forms of educational services, Happer accomplished his mission of bringing Christian higher education to China, though much of the student body of the training school included those working for the church. In order to reach governmental Chinese leaders through western education, from 1865 and 1867, Happer directed the Chinese government's Interpreter's College in Canton and taught English and mathematics to students entering government services as foreign specialists. By introducing Christian teachings within his courses, he continued his mission of evangelism and observed the gradual growth of Canton Presbyterians. This is supported by the statistics reported from the Canton Mission that in 1866: 147 individuals were enrolled in mission schools.