Academics from London South Bank University studied more than 600 children and found that those from minority ethnic backgrounds were more likely to end up in schools lower down in the league tables than their primary schools had been.
It found that Black Caribbean pupils do badly but Muslim pupils are the hardest hit.
Lead researcher Professor Irene Bruegel said: "In the transition some children go up and some go down. White children go up while minority ethnic children go down. The process of competition clearly does not serve minority ethnic children well."
She said this could explain why the performance of many Black boys deteriorates once they are in secondary school.
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