Founded in the early 1950s, the Burlington Mohawks found their footing in the Central Junior B Hockey League. After seven seasons in the league and two league championships, the team was transferred to the Niagara District Junior B Hockey League.
In the Niagara League, the briefly renamed Industrials won both the 1963 and 1964 league championships before dropping down to Junior C in the late 1960s.
In 1970, the Mohawks jumped back up to the Junior B level in the Mid-Ontario Junior B Hockey League. They were in the league for one season before the Ontario Hockey Association shifted them back to the Central Junior B Hockey League.
The Mohawks were renamed the Cougars in 1976 and stayed in the Central League for twenty-two seasons, from 1971 until 1993.
In 1981, the Cougars won their first Central League championship since 1958. They went on to face the Stratford Cullitons of the Mid-Western Junior Hockey League in the Sutherland Cup final. The Cougars won the series 8-points-to-4 to defeated the Cullitons and claim their only Sutherland Cup.
In 1987, the Cougars won their fourth and final Central League championship.
In 1993, the Central League was promoted to become the Ontario Provincial Junior A Hockey League, the Cougars made the jump with the league. The Cougars have yet to win an OPJHL title.
For the 2010-2011 season, the Cougars changed their jerseys and colour scheme to the double-blue, in commemoration of the 30th anniversary of their 1981 Sutherland Cup Championship.