During his second mission, Happer focused on education and evangelism. He was passionate about converting Chinese individuals to Christianity and converting society through providing education. In 1850, he opened a set of day schools to educate young Chinese boys in both western and Chinese studies. The schools faced difficulty attracting youth from the upper class who were enrolled in traditional schools that prepared students for the civil service examinations. By December 1853, Happer opened a day school for Chinese girls which offered courses in reading, writing, and economics. By the end of 1853,the first eleven students graduated from the boy's boarding school with two students devoting themselves to the Canton mission.
