He started his education in St. Xaviers School, Pakyong, East Sikkim and won a eventually Scholarship SAI to attend the Tashi Namgyal Academy in Gangtok. He went on to play for several school and local clubs in his home state of Sikkim. A stellar performance at the 1992 Subroto Cup brought him to the notice of the football establishment. Former India goalkeeper Bhaskar Ganguly spotted his talent and helped him make a move to Calcutta football.
In 1993, at the age of sixteen, he left school to join the professional East Bengal Club in Calcutta. In 1995, he moved to JCT Mills, Phagwara, which went on to win the India National Football League that year. Bhutia was the top scorer in the league, and was chosen to play in the Nehru Cup. He was named "1996 Indian Player of the Year" and has won numerous other awards since then.
In 1997 he returned to East Bengal, and became team captain in the 1998-99 season. Baichung Bhutia has the unique distinction of scoring the only hatrick in the Derby Clashes between East Bengal and Mohun Bagan, when he registered the same in East Bengal's 4-1 triumph in 1997 Federation Cup Semi Final. In 1999 he travelled overseas to play for Bury F.C. after unsuccessful trials with both Fulham F.C. and Aston Villa F.C.with the move improving his conditioning and strategy. In 2002 he returned to India and played for the Mohun Bagan AC for a year before returning again to the East Bengal Club, helping them to win the Asean Cup (Association of South East Asian Nations) Club Championship. He signed up to play for Perak, the Malaysian championship club, from August to October 2003 and returning to East Bengal for the regular season. He continued to play for East Bengal till the end of 2005-2006 season. In 2006, he joined Mohun Bagan AC and has remained with them since then. He has recently renewed his contract for a further two years from 2008 to 2010 with the Mohun Bagan. He played in the Goal 4 Africa match held in the Allianz Arena, Munich on 12 July 2008 for the Edu team led by Clarence Seedorf and scored twice.He scored twice in the AFC Challenge Cup against Turkmenistan. He was also selected as the most valuable player of the tournament.