Brown last week announced the end of a 19-year playing career in which he won 22 domestic trophies with Celtic, whom he left at the end of last season to take up a player-coach role at Aberdeen.
Capped 55 times by Scotland, Brown left Pittodrie following the departure of manager Stephen Glass in February and is now set to embark upon his first managerial role with Sky Bet League One Fleetwood.
"I'm delighted to have been named head coach at Fleetwood Town," Brown said on the club website. "It's a great opportunity at a really exciting club.
"I've always had a real desire to move into management and can't wait to meet the players and staff and get started. The hard work starts now – I'm now looking forward to getting on to the grass."
Brown broke through at Easter Road before a £4.4 million move to Celtic Park – which remains a record transfer fee between two Scottish clubs – where he won 10 Scottish Premiership titles and captained the sides which won four consecutive domestic trebles.
Fleetwood chairman Andy Pilley said: "After a thorough interview process it was clear Scott was the outstanding candidate and someone who's a born leader, a serial winner and incredibly serious about becoming a successful manager.
"We feel we are the perfect club for Scott to start his managerial career and he's the perfect person to lead us to a new era at Highbury Stadium - it's a hugely exciting appointment for Fleetwood Town."