The B.C.-based pulp and paper producer said the "time is right for a leadership transition" following the completion of the company's court-supervised restructuring.
Clarke will stay in the position through to June until a successor is found.
Catalyst Paper returned to the Toronto Stock Exchange in January under the symbol CYT, after being delisted from the market last March.
"Under his leadership, the company intensified its focus on stakeholder relationships which culminated in the rapid completion of a reorganization plan that significantly improved Catalyst's balance sheet and cost structure," said Catalyst board chairman Les Lederer in a statement.
Catalyst Paper manufactures printing papers, newsprint and pulp and owns three mills in B.C.