[1] He was elected as a Democratic-Republican to the Tenth Congress, serving from March 4, 1807, until May 1, 1808,[2] when he resigned to accept an appointment by President Thomas Jefferson as one of the Judges of the Supreme Court for the Territory of Michigan.

He lived in Fair Haven, Vermont while on parole from the British and later was exchanged and returned to his duties in Detroit in the Michigan Territory.

On April 30, 1821, Governor Lewis Cass and Judges John Griffin and James Witherell passed a new act that changed the name of the Catholepistemiad or University of Michigania to the University of Michigan, and put control in the hands of a board of trustees consisting of twenty members plus the governor.

After serving as a Supreme Court justice for nearly twenty years, Witherell resigned in 1828 to accept an appointment by President John Quincy Adams to become Secretary of the Territory.

[7] Witherell died at his home in Detroit on January 9, 1838, less than a year after the Michigan Territory's admission to the Union as a state.