The Scottish Executive is to run two seminars early in the new year to help various groups influence the design process.
It comes at a time when more than 300 new schools are being built or refurbished through the controversial public private partnership (PPP) scheme.
Despite providing modern buildings, they have been branded "bland" and "lacking in elegance" by a leading architectural expert.
The Executive wants to involve pupils, parents and teachers in the development process to make sure that councils do not repeat design mistakes of the past.
Education Minister Cathie Jamieson said both seminars would help form a blueprint for progress.
"We have just embarked on the first phase of the biggest-ever school building programme - a £1.15bn package of investment that will deliver 300 new or refurbished schools," she said.
"This is a once-in-a-lifetime opportunity to create not just new schools but new schools which pupils want to learn in, teachers want to work in and which communities feel proud of.
International workshop
"Two design workshops will be held early in the new year, backed by £30,000 of Executive cash, to develop future design ideas - one for children and one for architects, teachers and other key groups.
"The ideas will be published and will act as a template for those involved in school building projects."
Once these ideas have been collected, they will be shared on the internet through the national architecture website to provide a template for school building projects.
The two-day children's workshop at the Lighthouse in Glasgow aims to give pupils the chance to consider how the classroom of the future may look.
The workshop will bring architects from Scotland and abroad together to examine the connections between the quality of the built environment and learning objectives.
A School Estate Strategy is also being drawn up by the Executive and local authorities.
It will be published in the New Year and list key stipulations for schools on safety, suitability and security.