In a statement on the SPFL Premiership club's official website he intimated that the time is right for him to leave.
The Dens Park side have returned to the top flight in Scotland and are in the hands of a Texas-based consortium, a deal which Gardiner helped to negotiate last year. He also played a prominent role in securing Dundee's finances after the club fell into administration for a second time.
"I have greatly enjoyed my time at Dundee," said Gardiner. "I will miss everyone but I leave confident the club is in good hands."