Culkin was born in Manhattan, New York City, New York, the son of Philip Harley Culkin (1898–1977), who was in public relations, and Marian Ethel (née Wagner) (1914–1964), a Writer and Editor. He and his sisters Candice and Actress Bonnie were raised in New York City.

He has fathered eight children: Jennifer Adamson (1970–2000) with Adeena VanWagoner; Shane (b. 1976), Dakota (1978–2008), Macaulay (b. 1980), Kieran (b. 1982), Quinn (b. 1984), Christian (b. 1987) and Rory (b. 1989) with Patricia Brentrup (b. 1954). Culkin and Brentrup were together for 21 years from 1974–1995, but never married.

He and his sister Bonnie took classes at School of American Ballet (as did his son Macaulay in the late 1980s).

On December 9, 2008, Kit's daughter Dakota was struck by a vehicle when she stepped off a curb into its path. She was taken to UCLA Medical Center where she died at age 30 of her injuries the following afternoon. Culkin's daughter Jennifer Adamson died in 2000 (also at age 29) from a drug overdose.

Three of his sons — Macaulay, Rory, and Kieran — are professional actors whose careers eclipse their father's acting career but have gained him prominence as their manager from the late 1980s to the mid-1990s. In just a few years, the Culkin family went from modest means to wealth. Macaulay became extremely popular due to his starring roles in the Home Alone feature films, and he was the first child in Hollywood to receive a million dollar salary (for My Girl (1991)). From 1995 to 1997, Kit was part of a child custody trial.

Culkin resides in Grants Pass, Oregon. His long-time friend and partner, Jeanette Krylowski, died on May 31, 2017.