Lawyers for Victor Rosario, 57, argued that the 1982 investigation wrongly concluded the fire was deliberately set and that Rosario's confession was not voluntary. In an opinion issued Monday, Superior Court Judge Kathe Tuttman overturned Rosario's conviction and ordered a new trial.
"I conclude that the defendant has met his burden to establish that justice was not done in this case," she wrote in her 99-page decision.
The fire, which killed eight people, was the worst in the history of Lowell, a small city north of Boston once known as a textile manufacturing center.
The New England Innocence Project said that some of the markers investigators used as evidence of arson are now known to occur in fires that have not been deliberately set. In an analysis of Rosario's case, the project said the number of fires declared to be arson fell by 70 percent between 1988 and 2001.
Rosario had made previous appeals.
"He has said from the very, very beginning that he is innocent," Rosario's lawyer, Marian Petersen, said after Tuttman's ruling. "He has been fighting this for so long."
In one controversial case, Cameron Todd Willingham was executed in Texas in 2004 for a 1991 fire that killed his three young daughters. Experts arguing for a reversal of his conviction and sentence said the fire appeared to have been accidental.