After the war, he returned to Massachusetts to become Professor of Sacred Literature at Andover Theological Seminary, where he taught until 1882.

Thayer devoted nearly thirty years to the translation that first appeared in 1885, and updated edition in 1889.

[2] In February 1891 Thayer published a lecture in which he expressed disagreement with the position of biblical inerrancy, asserting that his own acceptance of various errors of history and science in the Bible did not materially detract from his belief in the overall soundness of Christianity.

In his 1895 presidential address, he called for the creation of an "American School for Oriental Study and Research" in Palestine.

[4] Over the next five years, the Society was involved in the establishment of the American School of Oriental Research in Jerusalem.