The Heritage Cup trophy was conceived and designed by San Jose Earthquakes fan Rob Stevenson and was commissioned by San Jose's Soccer Silicon Valley Community Foundation in collaboration with Seattle supporters. The competition began in 2009 when the expansion Seattle Sounders FC began play, becoming the second MLS team named after their NASL counterpart — the San Jose Earthquakes having been the first.
San Jose and Seattle did have a rivalry while playing in the NASL. However, it did not completely resurface during the 2009 season with fans of both teams viewing other clubs as bigger rivals. That season, the first MLS meeting of the teams was not considered for the competition due to the schedule consisting of two games in Seattle and only one in San Jose. Seattle won the initial meeting at home 2–0 and the second 2–1. The San Jose Earthquakes won the inaugural cup on goals scored after a 4–0 home victory on August 2, 2009.
Present and future MLS teams that carry on the name of their market's NASL predecessors are eligible to join the competition. However, when the Portland Timbers and Vancouver Whitecaps FC became eligible to compete for the cup upon joining the league in 2011, both teams' supporters elected not to participate. They left open the possibility of joining if a couple of additional eligible teams join the MLS, thereby better differentiating the Heritage Cup from the Cascadia Cup.
The 2012 MLS Season brought an unbalanced schedule for the first time since 2009. The rules to the cup therefore reverted to counting only the last two matches between the teams, the way it will be counted in any season that has an unbalanced schedule.