The commissioner said that she set "clear goals to reinvigorate enforcement at the bureau" when she took the job.
"With the help of the bureau's dedicated staff, I believe we have accomplished what we set out to do and positioned the bureau to continue its valuable work well into the future," Aitken said in a statement announcing her resignation effective Sept. 21.
Aitken joined the bureau in 2005 as assistant deputy commissioner of competition, mergers, and was appointed senior deputy commissioner in May 2007.
She served as interim commissioner from Jan. 12, 2009 to Aug. 4, 2009, before she was appointed as Commissioner for a five-year term.
Before joining the federal regulator, Aitken was a commercial litigation partner at law firm Bennett Jones LLP.
Aitken has been credited with pushing the Competition Bureau to take on an more active role in protecting consumers.
The bureau has launched a high-profile challenge to the merchant fees charged by credit card companies as well as other cases involving the Toronto Real Estate Board and Air Canada.
Last year, Bell Canada agreed to pay a $10-million fine for using misleading advertising on prices for its home phone, Internet, satellite TV and wireless services.
The fine was the maximum amount allowed under the Competition Act.
Industry Minister Christian Paradis thanked Aitken for her work.
"Thanks to her dedication and determination, the bureau is well recognized by businesses and consumers alike for ensuring that Canadian competition laws are respected," Paradis said in a statement.