Howson -- one of only two GMs in Blue Jackets history -- had held the job since June 2007, compiling a 173-190-59 record with one playoff appearance in 2009.
Last season, however, Columbus had the worst record in the NHL with 65 points and was off to a 4-7-2 start in the lockout-shortened 2012-13 campaign.
He traded the team's lone superstar, Rick Nash, last summer in a deal that earned much criticism from fans.
"Scott Howson is a caring man who gave everything he had to the Columbus Blue Jackets over the past six years," Blue Jackets President John Davidson said. "This was a difficult decision, but one that I thought was in the best interest of moving our hockey club forward."