Andrew Dixon will leave the post of chief executive of Creative Scotland at the end of January next year.
He is currently off on sick leave and and a crunch two-board meeting is due to be held later this week.
In October, more than 100 artists and writers, including national poet Liz Lochhead, author Alasdair Gray and crime writer Ian Rankin, joined forces to criticise the body.
In an open letter to the organisation's chairman Sir Sandy Crombie, they called for a fresh start, asking that Creative Scotland acknowledges the "scale of the problem" and commits to more stable funding for small arts groups.
It stated: "This letter is not about money. This letter is about management.
"The arts are one of Scotland's proudest assets and most successful exports. We believe existing resources are best managed in an atmosphere of trust between those who make art and those who fund it.
"At present, this trust is low and receding daily."
Mr Dixon said in a statement today: "It has been a privilege to have been involved in the early years of Creative Scotland and to have worked with such talented and dedicated staff, but I now feel the time is right for a change of direction for both myself and the organisation.
"I am proud of what has been achieved since the merger. We have delivered new resources for the arts and established strong partnerships with local authorities, broadcasters and many other agencies.
"The Year of Creative Scotland, The Guide to Scotland's Festivals, a new capital programme, the Creative Place Awards and the recent Luminate festival have shown the potential for all parts of Scotland to play a part in the creativity of the nation.
"I have been disappointed, given my track record, not to gain the respect and support of some of the more established voices in Scottish culture, and I hope that my resignation will clear the way for a new phase of collaboration between artists and Creative Scotland."
Mr Dixon thanked Culture Secretary Fiona Hyslop, Sir Sandy and the rest of the board.
He added: "The staff team at Creative Scotland is exceptional and, despite recent strains, they continue to demonstrate professionalism and a true passion for the artistic and creative life of Scotland.
"I wish them all the very best."
The process of finding a new chief executive will now begin.
Sir Sandy said: "On behalf of the board, I would like to thank Andrew for his stewardship of Creative Scotland since its inception.
"As a new organisation with an extensive remit, there have been inevitable challenges during this period and Andrew has consistently led the organisation with energy, passion and enthusiasm.
"He has also taken every opportunity to be a vociferous champion and advocate for Scottish arts and culture."
Before joining Creative Scotland, Mr Dixon was chief executive of the NewcastleGateshead Initiative, executive director of Arts Council England and Chief Executive of Northern Arts where he was centrally involved in developing projects such as the Baltic, the Angel of the North and The Sage Gateshead.
He previously worked in local government, young peoples’ theatre and in rock music promotion.