Principal Anne Coutts said the decision "strengthened the school's commitment" to single-sex education, after the former all-boys school Canberra Grammar famously opened its doors to girls in 2016.

That change ended a long history of co-operation between the two schools, which had both previously taken girls and boys up until Year 2 and then provided a reciprocal enrolment guarantee for Year 3.

As rumours swirled around campus on Wednesday morning, a Canberra Girls spokeswoman confirmed that, come 2020, boys would only be accepted into the early learning centre, which was also set to expand by 50 per cent.

"We're not saying boys already at the school will be asked to leave by then, except three-year-olds in our [program] right now, they won't be offered a place in prep."

Ms Coutts said the end of the school's historic partnership with Canberra Grammar had made for an "interesting year", but the decision came down to plans to take development programs for girls into younger year levels.

"Those programs are about giving girls a voice, making sure that they're resilient and that they believe they can make choices based on their own strengths, which you know is sometimes not the case when we have boys grabbing the attention.

"Our Year 5 program 'Girls with Grit' is now in its second year and we've just noticed such a difference already...so we want to extend those programs down into the junior school."

While the school had previously considered taking boys up to and including Year 3 in order to feed them directly into other local single-sex boys' schools, Ms Coutts said feedback from families had quickly turned them off the idea.

"We had some really impassioned parents saying 'please don't do it' which really it took us by surprise," she said.

"And it comes back to why we're really passionate about this, I've found with my own girls, both of them went to all-girls schools and they had so many opportunities.

"What happens in the workplace is potentially happening in [co-ed] schools but [at an all-girls] school they don't just get equal opportunity, they get every opportunity."

Despite some reports of girls leaving the school for Canberra Grammar, Ms Coutts said the break with the brother school had allowed Canberra Girls to flourish.

"We haven't really had [girls leaving], the biggest thing is we've launched our new Music Academy this year, which is open to a number of schools who don't have their own music program as well, and we already have a huge concert coming up.

"We wouldn't have been able to do that if we were still doing a joint music program with the boys' school."

Families affected by the decision had all been contacted as of 11:30am Wednesday, she said, when the school made a formal announcement.

"From 2020, Canberra Girls Grammar School will become the only prep (kindergarten) to year 12 all girls school in the region," a statement from the school said.

Ms Coutts said the school encouraged feedback from families but, so far, those affected had thanked them for allowing such a long notice period.

To accommodate long waiting lists, new classrooms will also be built at the school's award-winning early learning centre.