The Shamrocks were founded on December 15, 1886 at a meeting of the Shamrock Lacrosse Club to organize an ice hockey club. The Shamrock Lacrosse Club of Montreal predated the hockey team by twenty years, founded in 1867 by J. B. L. Flynn. Both teams were under the umbrella name of the Shamrock Amateur Athletic Association of Montreal. The Shamrocks started off playing exhibition games, but their standard of play increased leading to the club playing in two Amateur Hockey Association of Canada (AHAC) challenges, in 1891 and 1892 respectively. After these challenges the club went into dormancy, but in 1895 the SAAA purchased the Montreal Crystals' hockey club and merged them into the Shamrocks, reviving the team in the process. The newly revived Montreal Shamrocks hockey club then replaced the Crystals midway through the AHAC's 1895 season. After this, the club began actively competing in season based play.
The club rose to be the pre-eminent senior amateur hockey club in North America by the turn of the twentieth century, winning the Stanley Cup in 1899 and 1900 before losing a Stanley Cup challenge in 1901. Following the retirement of its stars, including Hall of Famers Harry Trihey and Arthur Farrell, the Shamrocks faded from prominence and never again had a winning season. They were eventually done in as a professional entity around 1910 by the growth of professionalisation in hockey. Despite playing one season in the National Hockey Association (the forerunner to the National Hockey League), they had trouble competing financially with other clubs, and with the myriad splits and feuding in elite-level hockey (which lead to the formation, disbandment, and formation of new leagues), the Shamrocks ceased being a professional club and became dormant.
In 1911–12, the club was reactivated and returned to their amateur roots by joining the Interprovincial Amateur Hockey Union. In 1912–13, they joined the Montreal City Hockey League. They played in that league until 1924 when the Shamrocks finally folded.