He was raised as a Roman Catholic in the predominately Protestant and Unionist town of Ballymena in County Antrim and later graduated from Queen's University of Belfast. When asked by an interviewer about his upbringing in relation to the Troubles, Neeson spoke of Ballymena as "a hardworking community that witnessed little of the sectarian prejudice that plagues much of Northern Ireland".

In fact, as a young man most of his friends were Protestants. However, on being offered "Freedom of the town of Ballymena" by Ballymena Borough Council, his subsequent comments that he had felt like a "second-class citizen" growing up in the town, resulted in the offer being withdrawn. At age nine, Neeson began taking boxing lessons at the All Saints Youth Club. Standing six feet four inches high, he became a youth champion before a blackout during one of his boxing matches forced him to withdraw from the ring.