After law school, Lynn continued to work with the United Church of Christ to gain amnesty for young men who chose desertion to protest the Vietnam War. Before going to Americans United, Lynn held positions related to religious liberties. In the mid-to-late 1980s he was legislative counsel for Washington's ACLU office, where he frequently worked on church–state issues. From 1974 to 1980, Lynn held positions within the national offices of the United Church of Christ, including two years for the Church's Office of Church in Society in Washington, D.C., as legislative counsel.