McGilligan is an Irish surname. It derives from Mac Giollagáin. Notable people with the surname include:
Brian McGilligan (born 1963), Irish hurler and Gaelic footballer Janak Palta McGilligan, Indian social worker Patrick McGilligan (Fine Gael politician) (1889–1979), Irish lawyer and politician Patrick McGilligan (biographer), American writer Patrick McGilligan (Irish nationalist politician) (1847–1917), Irish nationalist politician