Gourcuff began his career with FC Lorient, who were, at the time, managed by his father. During his time at Lorient, he also trained at the Pôle Espoirs Football de Ploufragan, a smaller version of the Clairefontaine Football National Academy. Further to his father's departure to Stade Rennais, Gourcuff, who initially considered Nantes, followed suit and signed an élite (youth) contract with the club in 2001. While in the youth system at Rennes, he participated in the Coupe Gambardella and scored a goal in their 4–1 demolition of Strasbourg in the final match helping the club win the 2003 edition of the youth cup.

As expected, Gourcuff signed his first professional contract in November 2003 and was promoted to the first team for the latter part of the 2003–04 season. He made his league debut on 7 February 2004 in a 0–2 defeat against Auxerre, coming on as a substitute in the 76^th minute. He made eight more appearances that season, which included his first start against Bordeaux in a 3–1 victory. The 2005–06 season was more successful for Gourcuff. Wearing the number 10 shirt, he appeared in 36 matches, scoring six goals, which included his first ever league goal against Monaco in a 2–0 win He formed partnerships with fellow Frenchman Olivier Monterrubio and the Swede Kim Källström, helping Rennes to finish 7^th in Ligue 1 and winning them a place in the 2006 UEFA Intertoto Cup.