Huggel grew up near Basel, completing training to be a landscape gardener before he became a professional footballer. He made his debut for FC Basel in December 1998.

In his first spell with Basel, he was a member of the team which won the League and Cup double in 2001/02, although he missed the Cup Final due to injury. His growing reputation was increased by the quality of his performances during Basel’s run in the Champions League in 2002/3, including the famous victory over Liverpool. Over the next two years, he was a regular as Basel won two more Swiss League titles.

In 2005, Huggel transferred to newly promoted German club Eintracht Frankfurt and in his first season he played 28 times and reached the DFB-Pokal Final, where Eintracht lost 1-0 to Bayern Munich. In June 2007, he was transferred back to Basel for €400,000, for whom he then played until he announced his retirement in July 2012, having won a career total of seven Swiss League Championships and five Swiss Cups.

Huggel played 41 times for the Swiss international team, making his debut in the 2-0 defeat by France in August 2003. He appeared in all three of Switzerland's European Championship group matches in 2004 and was in the team in all three group matches in the 2010 World Cup in South Africa.

After Switzerland failed to qualify for the knockout stage, he announced his retirement. He only received four yellow cards in his international career, a remarkable achievement for a defensive midfield player.