The Canadian military says it mistakenly rejected the application of a transgender woman from Brantford, Ont., over concerns related to her hormone replacement therapy.

Now, Canada's Armed Forces is changing the way it handles complex medical applications in an effort to make sure this same problem doesn't happen again, said Col. Jim Kile, director of medical policy.

"It was a misunderstanding we created, there's no way around it," Kile told CBC News. "For complex cases, whether they're transgender or otherwise, they're going to go to our senior medical office from now on.

"We don't want this to happen to transgender folks who are trying to get into the military, or anyone who is trying to get into the military with a condition."

The military's mea culpa comes a day after CBC News first published 24-year-old Kennedy McArthur's story. She applied to join the reserves in the Brantford 56 Field Artillery last summer, but was denied because she takes estrogen, the military said in a letter.

I feel more hopeful. I went home today feeling pretty good. - Kennedy McArthur

Kile said this was a mistake on the part of the Armed Forces.

"We never turn an applicant away based on the fact that they may be on hormonal replacement medication," he said.

Kile said he phoned McArthur on Wednesday to try to make the situation right.

"I phoned the applicant for two reasons. One was to explain what we did wrong, and two was to apologize for it, and to express to her that it was never our intent to hurt anybody," he said.

"Further to that I explained that we were simply going to go forward with putting in a failsafe within our process with the recruiting medical office to reduce that kind of mistake to as close to zero as we can get."

'I feel more hopeful'

McArthur told CBC News that she's cautiously optimistic about the military's position, and thinks she now has a genuine shot at making it into the reserves.

"I feel more hopeful. I went home today feeling pretty good," she said. "At the same time, I can't help but still have questions lingering, like why did this happen? I also hope that this isn't just putting a Band-Aid on an open wound. I'd like to give them more credit than that."

She said that part of the issue here is there does not appear to be a transparent, uniform policy for transgender people when attempting to join the military.

"I don't think anyone knows what [the issue] was, and no one was able to make that clear," she said.

"The whole thing was a mess. I do kind of feel like they're backpedalling, in a way."

All McArthur has to do now, Kile said, is provide some more information from her doctor. "Then we move forward," he said — though he could not speak to her situation specifically, citing confidentiality issues with her medical file.

McArthur said that as far as she understands, her doctor just needs to sign off on a testimonial saying that she can still provide the services required by the military, despite her use of hormones.

"And my doctor has already said there's no reason my use of this drug would debilitate my performance in the military," she said.

adam.carter@cbc.ca