Linehan was married to writer Helen Serafinowicz, the sister of actor Peter Serafinowicz; the couple have two children. In October 2015, Graham and Helen Linehan worked with Amnesty International on a campaign film calling on the Irish government to repeal the Eighth Amendment of the Constitution, which "acknowledges the right to life of the unborn and, with due regard to the equal right to life of the mother, guarantees in its laws to respect, and, as far as practicable, by its laws to defend and vindicate that right". The couple revealed their decision for Helen to abort a foetus with acrania while living in England in 2004, and their discovery that undergoing the procedure in Ireland would have been an offence carrying a maximum 14-year prison sentence. In 2021, Linehan said that he and Serafinowicz had separated following financial problems caused by his activism against the transgender community.