The draft Greater Manchester Low Emissions Strategy and Air Quality Action Plan suggests "flexible" days allowing pupils to avoid rush hours.
It also suggests more hybrid buses, better public transport and greater use of carpools and bicycles.
Other ideas include discouraging local authority staff car use.
The proposals are part of range of measures in a clean air strategy being analysed by the Greater Manchester Combined Authority.
"It is generally recognised that school travel can contribute significantly to local traffic, leading to congestion in some areas," a report said.
The report which is part of a continuing strategy being discussed by the authority and led by Transport for Greater Manchester  (TfGM) stated:
It added: "Potential means of reducing car journeys for school, or reducing the effects of the journeys, may include public transport subsidies, or flexible school days that allow pupils to arrive earlier or later and avoid peak travel times."
The report explained that Greater Manchester is currently breaching European Union levels for harmful emissions.
Helen Smith, Head of Logistics and Environment at TfGM, said the plan would be open to public consultation in 2016.
Avis Gilmore, north west regional secretary for the National Union of Teachers, said varying school hours took no account of school timetables and would be difficult for parents who had children at different schools.
She added: "It would be so disruptive."
School opening hours in Greater Manchester could be varied in a bid to cut road congestion and air pollution, an environmental plan has said.