He was educated at the City of London School, where he was the first boy to enter the new school in 1837 and became the first Times scholar at Cambridge. Admitted to Corpus Christi College, Cambridge in 1843, he graduated Bachelor as 5th Wrangler in 1847.
He was ordained in 1849 and was Fellow, Dean, Bursar and Tutor of his old college until 1865. From 1864 until 1907 he was Archdeacon of Ely, marrying Fanny Maria, daughter of Sir Antonio Brady in 1865. Emery had been present at the first meeting of the Church Congress in 1861, where he spoke on free church seats, diocesan associations for increasing benefices for the endowment of poor benefices, and church rates.
In 1869 he was appointed permanent Secretary of the Congress, and by 1907 had been present at every one of the first 47 Congresses.
He died on 14 December 1910 at Ely.