James Morton of the Equality Network said gender neutral lavatories reduced bullying and graffiti and were safer for young people.
The plans were outlined in Scottish Government guidance setting out the minimum standards for school buildings, which updates regulations first introduced in the 1960s.
The “Consultation Document on Updating the School Premises (General Requirements and Standards, Scotland, Regulations 1967)” said the existing regulations said half of toilet accommodation should be for boys and the other half for girls.
It went on: “The School Premises Regulations do not prescribe standards for accessible sanitary facilities for persons with a disability or refer to unisex toilets that could address gender issues. Therefore, the Regulation needs to be updated and simplified to meet current expectations.”
Critics of unisex toilets, which have a communal area for handwashing and cubicles, fear some pupils would be too embarrassed to use them and believe they could encourage sexual activity amongst youngsters.
But Mr Morton, Scottish Trans Alliance Manager, said unisex loos would be more suitable for transgender pupils.
He said: “We welcome the proposal from the Scottish Government to introduce gender neutral toilets across more schools in Scotland. A significant number of Scottish schools already successfully have gender neutral toilets. Schools have found that gender neutral private cubicles with open washing spaces reduce bullying and graffiti. Therefore, gender neutral toilets are safer for all young people. They are particularly beneficial for transgender young people because otherwise transgender pupils often fear going to the toilet so much that they refuse to drink liquids during the day and experience dehydration. Gender neutral toilets are not a radical new idea, they have been commonplace in schools and public venues across Europe for many years. Indeed, we all use gender neutral toilets every day without thinking about it - on planes, trains, and most importantly - in our homes.”