In 2012, Master-Cpl. Stéphanie Raymond accused Warrant Officer André Gagnon of sexually assaulting her a year earlier. Gagnon was acquitted by a military jury last August.
Raymond said she faced retaliation and harassment for coming forward with her allegations and was fired at the end of 2013.
Her appeal of Gagnon's acquittal is scheduled for 2016.
Gen. Tom Lawson sent apology letter
The Department of Defence released a statement on Thursday saying Col. D.A. MacIsaac would preside over the board of inquiry, an internal, non-judicial administrative investigation.
Her lawyer, retired Col. Michel Drapeau, said the board of inquiry is the only thing that will prevent the CAF from repeating its mistakes.
He said that while Raymond is pleased with the convening of the board, she would rather the hearing be held in public.
That will not happen, as such boards of inquiry are held behind closed doors. However, she will be provided with the board's findings.
In December, Chief of Defence Staff Gen. Tom Lawson sent a letter to Raymond in which he admitted she had been badly treated by higher-ranking officers in her regiment.
Lawson also said in that letter that Raymond had been fired based on falsified information and that the documents used to dishonourably discharge her were not in accordance with military firing procedures.
Lawson said the chain of command had failed Raymond.
As part of the military’s response to Raymond’s grievances, her dishonourable discharge was reversed, and she was retroactively promoted from corporal to master corporal, even though she had already left the military.
Her request for $85,000 compensation plus $15,000 for her spouse is still the subject of negotiations.