Insp. Ronald Makar faces one count of sexual intercourse with a female without her consent and one count of having sexual intercourse with a female under the age of 14.
Makar was arrested at the Wood Buffalo RCMP detachment in Fort McMurray, Alta., where he was operations officer in charge.
RCMP say Makar has been a Mountie for 34 years and served at the Carlyle, Sask., detachment as a constable in 1982.
Police say a woman filed a statement last year alleging that she was assaulted in the summer of 1982 by a man and a woman.
Makar has been suspended with pay.