Malcolm replaces former boss Ian Little who departed the club last week.
Malcolm, 41, was most recently with Forfar Athletic and also has experience of successfully managing in the Lowland League having led East Kilbride to a title back in 2019.
A defender during his playing days, he enjoyed an esteemed career on the park which included spells at Ross County, Drogheda United, Dublin City, Alloa Athletic, Shelbourne, Finn Harps, Arbroath and Stenhousemuir amongst others.
His tenure at Forfar represented a fourth spell at Station Park, having already been with the club as a player during three different spells and establishing himself as a fan favourite.
Club Chairman, Brian Porteous said: “Myself and the Board of Directors are delighted to welcome Stuart to the club.
“When conducting the search for a new manager, we knew the importance of finding someone who could make the most of the support that we offer them as a board; a leader that would match the club’s ambitions.
“We were looking for someone well-respected in the game, and someone who can get the best out of the playing squad with plenty of contacts in the game to help further strengthen the playing squad, push us towards better performances and achieve progression on the park.
“We were extremely impressed with Stuart’s thoughts and ideas when speaking to him, and we’re confident that he fits this bill. We believe he’ll fit in brilliantly at Shielfield Park, and are proud to have him lead the club.”
New manager Stuart Malcolm said: “I’m absolutely delighted for the opportunity to build, progress and evolve the club and cannot wait to get started.
“Berwick should be and need to be fighting higher up the league table, which I have been brought in to do with my experiences of this league.
“I’m looking forward to the league starting and getting time to work with the players through pre-season to implement my style of play.”
Malcolm will confirm his backroom staff over the next few days, and was at Shielfield to meet the squad for the first time on Tuesday .