After a brief stint as president of Jefferson College in Pennsylvania, Breckinridge returned to Kentucky, where he pastored the First Presbyterian church of Lexington, Kentucky, and was appointed superintendent of public education by Governor William Owsley. The changes he effected in this office brought a tenfold increase in public school attendance and led to him being called the father of the public school system in Kentucky. He left his post as superintendent after six years to become a professor at Danville Theological Seminary in Danville, Kentucky.