The union surveyed nearly 500 teachers working in schools around the UK, and 70 per cent said transport problems meant children could have difficulties even getting to school.
In total 77 per cent of teachers said transport problems meant pupils couldn't take part in after-school activities and 50 per cent said lack of transport stopped parents going to parent meetings and school events.
And many fear poorer pupils would not be able to take diplomas because they could be unable to get to further education colleges.
Dr Mary Bousted, general secretary of the ATL, said: "The government must stop ignoring the countryside. Poverty does not stop at the edge of our towns and cities, and before the government makes any policies or changes existing ones it must stop and think about the impact they will have on families living in rural areas.
"The diploma programme could fail in the countryside if children cannot get to the colleges running the courses. We cannot allow this situation to continue."
Other issues affecting children in rural areas include isolation and a lack of employment opportunities and apprenticeships, ATL said.
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