Two Wellington colleges are meeting the needs of transgender students by installing gender neutral bathrooms.

For thousands of youngsters who identify as transgender, choosing whether to use male or female bathrooms can be a struggle.

"That can be quite an unsafe space for that young person, either just from the verbal harassment or feeling like they don't belong, through to actually being bullied or beaten up," Rainbow Youth's Duncan Matthews says.

Onslow College is about to upgrade some female toilets to a gender neutral space, which will be available for all to use.

The $50,000 plan has been signed off by the college's board.

"They're bathrooms students can use where they feel that's appropriate for them rather than feeling uncomfortable going into a labelled bathroom," principal Peter Leggat says.

Wellington High School was the first to introduce gender neutral bathrooms.