Kit Harington was born Christopher Catesby Harington in Acton, London, to Deborah Jane (Catesby), a former playwright, and David Richard Harington, a businessman. His mother named him after 16th-century British playwright and poet Christopher Marlowe, whose first name was shortened to Kit, a name Harington prefers. Harington's uncle is Sir Nicholas John Harington, the 14th Baronet Harington, and his paternal great-grandfather was Sir Richard Harington, the 12th Baronet Harington. Through his paternal grandmother, Lavender Cecilia Denny, Kit's eight times great-grandfather was King Charles II of England. Also through his father, Harington descends from politician Henry Dundas, 1st Viscount Melville, the bacon merchant T. A. Denny, clergyman Baptist Wriothesley Noel, merchant and politician Peter Baillie, peer William Legge, 4th Earl of Dartmouth, and MP Sir William Molesworth, 6th Baronet.

Harington was a pupil at the Southfield Primary School from 1992 to 1998. When he was 11, his family moved to Worcestershire, and he studied at the Chantry High School in Martley until 2003. He became interested in acting after watching a production of Waiting for Godot when he was 14, and he performed in several school productions. He attended Worcester Sixth Form College, where he studied Drama and Theatre Studies, between 2003 and 2005. When he was 17, he was inspired to study acting in a drama school after watching a performance by Ben Whishaw playing Hamlet in 2004. He moved back to London when he was eighteen and a year later attended the Central School of Speech and Drama, from which he graduated in 2008.