If the ideas are taken up, urinals would be a thing of the past and privacy would be protected.
Campaigners say crumbling facilities damage pupils' health and well-being.
They say school toilets are recognised as being a troublespot for bullying, with some children avoiding going, possibly leading to continence problems.
The recommendations cover schools being rebuilt or refurbished under the government's £45bn Building Schools for the Future programme.
Tim Byles, chief executive of the Partnerships for Schools, the agency responsible for the programme, said behaviour could be improved by good design.
"Toilets are recognised as a hotspot for bullies to threaten and intimidate others," he said.
"This is clearly unacceptable. The new standard specifications for toilets in schools means that cramped, dirty and vandalised toilets can become a thing of the past.
