He has been appointed Mark Roberts' successor after the former Partick Thistle and Ayr forward departed Hampden at the end of last year.
McKinnon had been out of football since being dismissed from the Bairns in the wake of a 1-1 draw at Dumbarton with growing supporter unrest and the team off the pace sitting fourth in League One after relegation from the SPFL Championship last May.
He was replaced by former Bairns players Lee Miller and David McCracken who were appointed to the job on a permanent basis to the end of the season, last month.
McKinnon took over at Falkirk in contentious circumstances having left Morton and a subsequent grievance raised by the Greenock side over the move saw the Bairns fined £60,000 for inducement.
He previously took charge of Brechin City, Raith Rovers and Dundee United where he had success as a midfield player. He was also a performance school coach in Dundee with the SFA.
He takes over at a pivotal time in the Spiders' history with the famously amateur club voting to turn professional and preparing to move from their Hampden home to Lesser Hampden next-door later this year.