Stewart has held several senior positions with CMHC, including his appointment as vice-president, regional operations and assisted housing in 2012.
Karen Kinsley steps down from the top job at CMHC on June 16 after 25 years at the organization and 10 years as president and chief executive.
A search for the next permanent president and chief executive is underway.
Earlier this year, Finance Minister Jim Flaherty tabled changes to place CMHC under control of the Office of the Superintendent of Financial Institutions.
CMHC provides mortgage loan insurance and related services.