The Cost of the School Day project has been created to make sure pupils from poor backgrounds are not excluded from activities or treated differently.
And organisers plan to work with pupils to find out how they are affected by poverty.
Louise Falconer, principal policy officer at Glasgow City Council, said: "It was the council's manifesto to develop an anti-poverty strategy and the Cost of the School Day project is part of that.
"We don't want any pupils to feel excluded from school because of their family circumstances.
"Exlusion can take place in a variety of ways, even when teachers are being well meaning.
"For example, we had a school that used a £100 surplus to buy stationery for pupils who couldn't afford their own.
"But then that stationery marked out the pupils who had it as poor and none of the children would use it."
The project has been developed by the Poverty Leadership Panel's child poverty group.
The idea of "poverty proofing" the school day was developed in England by the North East Child Poverty Commission and the Glasgow scheme will use that as a model.
Education bosses believe poor children can be left out at school or bullied.
Unintentional discrimination in schools can mean children living in poverty are marked out as being different from their peers, such as not being able to afford to go on school trips.
It is hoped the new scheme will challenge and change these behaviours.
Policy experts will investigate how schools impact on children and young people experiencing poverty.
They will question staff and pupils on school policies and practice, about topics such as the cost of uniforms, how many children have a ccess to the internet at home, how homework is set and the opportunities young people have outside of the classroom.
Wider issues will also be looked at, from children coming to school without breakfast, to the knock-on effect of practices such as non-uniform days and charity collections and the number of children who attend school trips or take part in extra-curricular activities.
The delivery of free schools meals will also be discussed.
Each city school will be given recommendations to put into practice that will help stop children feeling - or being - marginalised.
And these recommendations will be tailored to each specific school.
Initially the scheme will be rolled out in two clusters: Smithycroft Secondary, Royston Primary, Ashcraig Secondary and Avenue End Primary; and Cleveden Secondary, Abercorn Secondary, Caldercuilt Primary and Kelvindale Primary.
Louise added: "We have chosen two sets of schools that cover quite different catchment areas. You might think that in a more affluent area pupils aren't affected by poverty but, actually, the reality can be worse for them because the gap between rich and poor is so much wider.
"It makes the stigma far worse."
A project coordinator has been employed to run the scheme, which will cost £50,000, for the next 15 months.
Councillor Stephen Curran, executive member for children and young people, said: "This project has been developed to make sure that no child is unintentionally left behind at school through poverty.
"Officers will work closely with young people and schools to ensure to all elements of the school day are looked at to ensure we "poverty proof" the school day for all our pupils.
"We are dedicating to listening to the views and requirements of our pupils as we work towards addressing their needs."