The Ayrshire haulage firm boss was co-opted onto the board in June 2010 to allow him to set up his 10000Hours project that aimed to buy out a consortium of directors selling a 51 per cent stake in the club.
But after finally lodging a £1.25million bid last September, the offer was rejected when the consortium - which included chairman Stewart Gilmour - expressed doubts about its "sustainability".
Atkinson will now step down from his boardroom role to focus on his work with Supporters Direct Scotland and their efforts to encourage fan ownership with Scottish clubs.
Press Association Sport also understands that the current board requested that he stand down because they feared his presence as a director may have put off other potential bidders.
The consortium put their controlling stake in the club up for sale four years ago but have so far failed to find a buyer.
In a statement, Atkinson said: "My involvement with the club came as a result of leading a proposal to buy the shareholding currently held by a consortium of the current board using a Community Interest Company which would in turn be owned and controlled by the fans of the club who were the members of the CIC.
"The final conclusion of the 10000Hours bid was unsuccessful despite a magnificent effort from the supporters for the proposal.
"I obviously wish the club well and in particular wish to thank the board, staff, team, management and of course the great fans for their support during my board membership.
"There are many others worthy of thanks but I shall make those thanks separately. All the best to Danny and this season's squad on the campaign to come."