The 29-year-old centre-back has agreed an 18-month deal after falling out of the first-team picture at the Highbury Stadium under Graham Alexander.
His last appearance came in the 3-2 FA Cup defeat to Aldershot on December 1 that cost Alexander's predecessor Micky Mellon his job.
McNulty was a vital member of the side Mellon led to two promotions in three seasons and into the Football League for the first time in the club's history after joining from Barrow in summer 2009.
Chairman Andy Pilley paid a glowing tribute to the 29-year-old in a club statement.
"I'd like to put it on record, that we wish Steve the very, very best at Luton Town," he said. "He's been absolutely fantastic and one of the best players in my nine-year era at Highbury.
"He's been hugely influential - both on and off the pitch, played an enormous part in us winning two promotions and he's just been superb.
"I think a lot of people don't realise just how good of a footballer he really is and what a good lad he is.
"He makes the manager's job an awful lot easier because he too won't accept defeats or draws and wants to win every single game.
"I cannot speak highly enough about him and he's always welcome at Highbury. I will be eternally grateful for everything he's done for Fleetwood Town."