The complainant, a woman from Saskatchewan, would have been 12 years old at the time of the alleged offences.
Makar, 54, has been charged with having sexual intercourse with a female person without her consent and having sexual intercourse with a female person who was under the age of 14.
Constance Haduik, 57, of Kyle, Sask., has also been charged with a sex offence involving the same person. RCMP say she was in a relationship with Makar in 1982 and that they were known to the alleged victim.
Haduik was arrested April 10 and charged with indecent assault of a female person.
Makar was arrested Tuesday at his workplace in Fort McMurray, where he has been in charge of the Wood Buffalo detachment.
He and Hadiuk are scheduled to appear in court in Carlyle, Sask., on June 4.
The charges were disclosed in Regina Tuesday by RCMP Supt. Alfredo Bangloy, who commended the alleged victim for her bravery in coming forward, but also noted it wasn't easy for him to speak to the media under such circumstances.
"It is very difficult to be here today," Bangloy said.
Makar has been suspended from his duties with pay pending the outcome of the charges against him.
The 34-year RCMP veteran spent most of his career working in Saskatchewan, serving in Carlyle, Fond du Lac, Milestone and Regina.
At the time of the alleged offence, Makar was in his first year as an RCMP constable, stationed at Carlyle, which is in southeast Saskatchewan.