Franklin joined the faculty of Tokyo Christian University as Professor of Philosophy and Theology in 1991. He was later elected, by the faculty and board of Tokyo Christian Institute, as Dean of the Faculty for a two-year period, and President of Tokyo Christian University in 1998. Franklin was re-elected President for a second term in 2002. He stepped down from this post in March 2006. Since stepping down as president, Franklin has been contributing to the advancement of higher education in Japan and the United States as Professor of Theology and Philosophy at Tokyo Christian University and Olivet Nazarene University.