It's a move to split responsibility at the top of the agency at a time when concerns like Ebola have put the organization in the spotlight.
As president, Outhwaite will manage the agency and its day-to-day operations, while Dr. Gregory Taylor, the chief public health officer, remains as the top health professional.
The reorganization was approved by Parliament earlier this year.
Outhwaite had been the agency's executive vice-president and chief operating officer.
She began her government career with the Fisheries Department in 1996 as director of inspection for the Pacific region.
She spent 10 years with the Canadian Food Inspection Agency and was an assistant deputy minister with Agriculture Canada from 2007 to 2009. She was named an assistant secretary to the cabinet in 2009.
She joined the public health agency in October 2010.