He took the President of Princeton University position in 1823. In 1824, he helped to create the Chi Phi Society, a semi-religious, semi-literary organization, which ceased activity the following year when it merged with the Philadelphian Society. During his tenure, enrollment increased from 70 to 250. After retiring in 1854, Carnahan served as a trustee of the college and as president of the board of trustees of the Theological Seminary. He died in Newark, New Jersey.