Though a separate entity, the league shared a commissioner, president, and director of umpires with the American Association of Professional Baseball.

The Allentown Ambassadors folded days before the 2004 season began, forcing the Northeast League to field a traveling team called the Aces.

For the 2005 season, the Northeast League accepted the Worcester Tornadoes as a new eighth team.

Floyd Hall Enterprises, which owned the Jackals, decided to launch a second team after the New Jersey Cardinals franchise was relocated and founded the Sussex Skyhawks.

The Skyhawks took the place of the Elmira Pioneers, which moved into the amateur New York Collegiate Baseball League.

After the 2007 season, the New Haven County Cutters and North Shore Spirit ceased operations.

[1] Later, however, the Commissioner stated the need for a "fresh start" and opened a contest to select a new name for the team.

[3] The Nashua Pride franchise was sold and was known in 2009 as the American Defenders of New Hampshire because of the military tie-ins of its new ownership group.

During the 2009 season the Defenders were locked out of Holman Stadium and forced to play their last home games on the road, bringing doubt to the future of baseball in Nashua.

Pittsfield's franchise charter was rescinded after the 2011 season and the Colonials folded after ownership could not find partners.

The Brockton Rox moved to the Futures Collegiate Baseball League after the 2011 season.

At the end of the 2012 season the Worcester charter was rescinded and the league decided to try to find new owners for the Tornadoes, but failed to do so and awarded the franchise instead to a Trois-Rivières, Quebec, group.

Beginning in 2012, Can-Am League clubs played 18 to 20 games per season against opponents from the American Association of Professional Baseball, with which it shares a commissioner.

The league later announced it would be returning to Sussex County, New Jersey as well, and announced that a traveling team would join the Ottawa Champions and the Sussex County Miners to create a balanced schedule, and continued to include matchups with the American Association.

Interleague play ended after the 2015 season, though the Can-Am League continued to send players to the American Association's All-Star Game.

[7] The Jackals, Boulders, Capitales, Miners and Aigles all joined but did not start play until 2021 due to the COVID-19 pandemic causing the league to cancel its 2020 campaign.

The two teams that were leading their respective divisions, designated North and South, at the end of the first half of the season automatically qualified for the playoffs.

This changed in 2015 when Ottawa and Sussex County joined the league, which enabled it to have enough teams to return to its previous playoff format.

The league salary cap was a maximum amount that could be spent on the entire player roster.