McGlynn, 50, was employed as a coach by Hearts for a decade but left six years ago to move into management with Raith.
He led the Second Division side to promotion, before establishing them in Scotland's second-tier First Division and taking The Rovers to their first Scottish Cup semi-final in 2010.
Rovers finished seventh in the First Division last season and McGlynn takes the reins at Hearts for a third time in his career, having briefly acted as caretaker following the departures of John Robertson and George Burley in 2005.
Hearts were without a manager after Portuguese coach Sergio failed to agree terms on a new contract despite winning the Scottish Cup in his first season.
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