Nieuwendyk was dismissed after the Stars concluded a 22-22-4 season with a fifth consecutive loss.
"Joe Nieuwendyk has represented the Dallas Stars extremely well as the club's general manager and has helped put pieces in place that will once again turn this team into a contender," team owner Tom Gaglardi said in a statement.
"I would like to thank Joe for his contributions to this hockey club and wish him and his family only the best in the future."
Nieuwendyk, a former Hall of Fame player, sparked the team during a 1998-99 run to their only Stanley Cup championship and served as GM for four years.
His replacement will be Detroit Red Wings assistant General Manager Jim Nill, Canadian broadcaster TSN reported.
He will be introduced Monday as the Stars' new GM, the report said.