John C. Young was born in Greencastle, Pennsylvania on August 12, 1803 to John and Mary Clarke Young. His father and his uncle were Presbyterian ministers, and he quickly determined to follow that course. To that end, he was educated at home and then at a classical school in New York City, before entering Columbia College there. After three years at Columbia, he withdrew and entered Dickinson College in Carlisle, Pennsylvania, where he graduated with the class of 1823.
Young spent the next three years at the Princeton Theological Seminary in New Jersey, tutoring there for another two years. He was licensed in the New York Presbytery in 1827 and the following year received an appointment to the McChord Presbyterian Church in Lexington, Kentucky. James McChord had been the first president of nearby Danville College and, by 1830, Young's reputation had grown sufficiently that he too was offered that post following the resignation of Gideon Blackburn. Still in his twenties, Young found the eleven-year-old institution, now called Centre College, in danger of extinction. In the next twenty-seven years, he brought the graduating class up from two to forty-seven and helped bring a reputation and relative prosperity to the institution as a foundation for the following century. Young continued to preach in the Danville church and served as moderator of the Kentucky Presbyterian Synod and the General Assembly of the United States in 1853 when it met in Philadelphia. He held with the Old School during the division in the church and himself was a slave owner. Young preached gradual emancipation rather than abolition - he twice freed families of his own slaves - and authored a report to the Kentucky Synod on the subject.
Young married Frances Breckinridge in November 1829. She died in 1837, and Young married for a second time to Cornelia Crittendon in 1839. Of his ten children, one, William C. Young, served as president of Danville. The elder Young began to suffer poor health and on June 23, 1857, John Clarke Young died in office at Danville College. He was fifty-three years old.