The equipment and changes to the terminal will cost up to $12 million, said Joe Handley, minister responsible for transportation, but the federal government will pay the bill.
Jim Winsor, director of the transportation department's airports division, said the X-ray system will be similar to the one that screens carry-on luggage.
He said it will be relatively fast, and will examine baggage for any items or substances that look suspicious. If something unusual is detected, the bag will be manually checked.
The Canadian Air Transport Security Authority issued new security requirements for 89 airports across Canada in the wake of the 2001 terrorist attacks in the U.S.
Yellowknife is the only one of 27 public airports in the Territories affected by the new security measures, Winsor said.