The 2012–13 Gil Vicente F.C. season was the club's 80th competitive season, 16th in the Primeira Liga, and 88th year in existence as a football club. As well as competing in the Primeira Liga, Gil Vicente took part in the Taça de Portugal and the Taça da Liga entering at the third and second rounds respectively. They were eliminated in the quarter-finals of the Taça de Portugal following a 2–1 away defeat by Paços de Ferreira. The Gilistas were eliminated in the second round of the Taça da Liga following a 3–2 aggregate loss by Naval 1º de Maio. Gil Vicente finished in 13th place in the league.