Despite his poor study habits, his talent in mathematics enabled him to graduate with first-class honors and remain at Christ Church as a lecturer, a position he held for twenty-six years. His original intention had been to enter holy orders, which was a condition of his residency at Christ Church. He became a deacon in 1861 but declined to pursue the priesthood. The dean allowed him to remain at the college, despite the refusal being grounds for dismissal from his position. Carroll recorded in his diaries that he felt he was a sinner who was unworthy of the priesthood.

