Kit's ancestry is English, as well as Welsh, Scottish, Northern Irish, and Dutch. His distant roots include German, French, and Spanish, and, going back to the 1400s and 1500s, he also has remote Italian, Polish, Lithuanian, Austrian, and Danish ancestry.
Harington was born on 26 December 1986, in Acton, London, to Deborah Jane (Catesby), a former playwright, and Sir David Harington, 15th Baronet, a businessman. His full name is Christopher Catesby Harington; his mother named him after Christopher Marlowe, whose first name was shortened to Kit, a name Harington prefers. He did not learn what his full name was until he was eleven years old. Harington's uncle was Sir Nicholas John Harington, 14th Baronet, and his patrilineal great-grandfather was Sir Richard Harington, 12th Baronet. The Harringtons are an ancient family that once spelled their name Haverington and derived the name from their estate, a lordship in Cumberland. The first person identified with their name was one Robert De Haverington, the son of Osulphus or Oswulf whose manor was Flemingby. Through his paternal grandmother, Lavender Cecilia Denny, Harington's eighth-great-grandfather was Charles II of England. Also, through his father, Harington descends from Scottish politician Henry Dundas, 1st Viscount Melville.
He is related to men who were involved on opposite sides of the Gunpowder Plot. He claims a family connection with the leader of the plot Robert Catesby on his mother's side, while through his father's side, he is related to James I (grandfather of Charles II), the target of the assassination attempt, and to Lord Harington, who was in the Houses of Parliament that Catesby and his co-conspirators tried to blow up. Another relation, John Harington (a different branch of the family), observed at the age of 13 the displayed head of Catesby after his execution and later commented on it.
At the age of four, Harington nearly drowned when he got into trouble in a swimming pool. In an interview with the Sunday Times Culture magazine, Harington revealed that he was "seconds from death".