Speaking after the decision CBC news reported that she said: "For the first time in quite some time, she was able to use the bathroom alone and so that made her feel wonderful."
Edmonton Catholic school had previously banned the child, who had been born male but identifies as female, from using the girls toilets.
Her mother said: "Is this a today solution and then next year it's a different solution? I'm very torn."
She had also praised school trustee Patricia Grell who spoke out criticising the board's decision contrary to board policy.
"No parent wants to have the conversation with their child about encouraging them wanting them to live and encouraging them that they are not a disgrace to God.
"So you go and you pray in your own sanctuary and here comes Patricia Grell. The answer to my prayers."
The school board released a statement saying that it will create a new bathroom policy in consultation with the Archdiocese of Edmonton, medical specialists, parents and educational experts.
However it will be decided on a case-by-case basis according to the school.
The board said: "In keeping with Catholic theology and philosophy, the board considers that this individual circumstance is best addressed on an interim basis at the school level."
However on-lookers have not been as optimistic, Kristopher Wells, from the Institute for Sexual Minority Studies and Services at the University of Alberta, said: "Given this non-decision today, I don't know how seriously we can take them at their word."
Transgender activist Marni Panas also questioned the willingness of the board to move forward and make progress, saying: "What saddens in all this though is it took this much public pressure for that statement to be made.
"I can't imagine a child being brave enough to come out and share what they have to share given all the stuff that's happened over the last few months."
Patricia Grell is thought to face an uncertain future after speaking out in support of the child.
The Catholic board scheduled a special meeting Tuesday to deal with "the public nature of board business," but abruptly cancelled it when "the mover of the intended motion advised that she wished to withdraw that single item," a news release said.
The mother said she will keep complaint open until the board says in writing that a her child will have access to the girls bathrooms throughout her school life.
