Charles Frederick Schaeffer (3 September 1807 in Germantown, Pennsylvania – 23 November 1879 in Philadelphia) was a Lutheran clergyman of the United States.

He was culturally ill-suited for this position, and, after difficulties with a colleague, students and other ministers and pastor, he responded to a demand that he resign.

There his conservatism was a challenge to liberal colleagues like Samuel Simon Schmucker and middle-of-the-roaders like Charles Philip Krauth.

As representative of the strictly conservative and confessional party in the Lutheran Church, Schaeffer defended his position with great force in many publications, and was a leader in the organization of the general council in 1867.

He published a large number of historical, homiletical, and doctrinal articles, and left several manuscripts of value, including a complete System of Lutheran Theology.