His brother was the priest and writer George Waddington.
Waddington was educated at Charterhouse School and Trinity College, Cambridge, where he was Bell Scholar in 1817, a Scholar and Pitt Scholar in 1818, Porson Prizeman for 1819, and winner of the Chancellor's Medal and 18th wrangler in 1820.
A barrister, Waddington was called to the Bar by Lincoln's Inn in 1825 before joining the Midland Circuit.
He was Recorder of Warwick and of Lichfield from 1838 to 1848, when Sir George Grey appointed him Permanent Under-Secretary of State for the Home Department, where he remained until 1867.
The Waddington Scholarship at the University of Cambridge was set up by his sister in the memory of him and his brother George.