Two-thirds of pupils in the UK feel that boys are "picked on" by teachers while girls and able students are treated better.
Research in five European countries found that 66 per cent of UK pupils believe that teachers had "pets" who received preferential treatment.
This was higher than any of the other countries covered by the Cardiff university study, except France, where 67 per cent complained about favouritism.
The study found that only 55 per cent of UK pupils felt that when their peers were punished they deserved it, compared to 69 per cent in Belgium, 63 per cent in Italy, 60 per cent in France and 57 per cent in Spain.
One girl told researchers: "It is mostly the boys in my class who get picked on or punished by teachers. This is because they have been bad in the past and the teachers immediately have a bad impression of the boys.
The teachers favour the girls and treat the boys unfairly."
Children in the UK were also most likely to report that teachers did not respect pupils. More than half said that teachers did not respect some children. "Some teachers in the school do not respect you, then you are told off for not respecting them," a boy attending a rural comprehensive said.
Two-thirds of pupils in Belgium, Spain and Italy, and 56 per cent in France said teachers respected everyone.
Emma Smith and Stephen Gorard, who carried out the survey, questioned 1,000 13 and 14-year-olds in each of the countries.
They said their findings raised questions for the teaching of citizenship.
"How can issues of fairness and democracy be effectively implemented if the students themselves do not believe their teachers are generally capable of such behaviour?" the report asked.
The study also found that more than 80 per cent of UK pupils believe that for schools to be fair, all pupils should get the same attention. But pupils in France, Belgium, Spain and Italy were more likely to think that the least able should get most attention.
Eamonn O'Kane, general secretary of the National Association of Schoolmasters Union of Women Teachers, expressed concern that some students felt teachers were unfair, but added: "Teachers are human. It is not really surprising if they have more sympathy for pupils who pay attention and work hard in class."