Huggel began his youth football with local club FC Münchenstein and came through the ranks between 1987 and 1996. He was loaned out to FC Arlesheim for two years (the price of which was a match ball), before completing his move to FC Basel in 1998. In his first year in Basel, under Manager Guy Mathez, he was solely a reserve player. Huggel made his debut for Basel on 6 December 1998, as he was transferred in during the 65th minute, in the 2–1 away win in the Wankdorf Stadium against Young Boys. In the 1998–99 season he made just three short appearances as substitute in the first team. But during the following year in the 1999–2000 Nationalliga A, under new Manager Christian Gross, he advanced into the starting team and played 34 of the 36 league games, scoring four goals. He scored his first goal for the team on 15 August 1999 as Basel won 2–0 against Luzern at home in the Schützenmatte Stadion. Huggel enjoyed his best campaign in 2000–01 when he scored eight goals in 29 league games from the centre of midfield.