Belanger said the decision to announce the $50 million was made three weeks ago, but officials had been talking about giving to Education Cannot Wait for months.
He said the organization operates in Jordan, Lebanon and South Sudan, and in camps where people have been displaced by the west African terrorist group Boko Haram, for example.
"We think it's important for girls to continue their education and that's why we're moving forward," he said.
Trudeau's principal secretary, Gerald Butts, took to Twitter to defend the move.
"This money is going to educate women and girls in the developing world, in commemoration of Nelson Mandela's 100th birthday," he tweeted