Flaherty, who has had the job since 2006, said Tuesday he is returning to the private sector.
He has battled a rare skin disease over the last year but he says his decision to leave politics is not related.
Prime Minister Stephen Harper's Conservative government plans on entering an election next year with a budget surplus.
Canada's commodity-rich economy avoided the worst of the 2008 financial crisis and has fared better than other nations. There was no mortgage meltdown or subprime crisis in Canada, and Canada's banks are rated among the soundest in the world.