Pierluigi Valencia was forced out of the school because his skin condition made it unbearable for him to wear regulation flannel trousers, the Disability Rights Commission claimed.
In a case due to be submitted today to a tribunal, it has accused the school of breaching the Disability Discrimination Act which requires it to make "reasonable adjustments" to accommodate disabled pupils.
The case is the first of its kind to be taken up by the commission, a government-funded independent body comparable to the Equal Opportunities Commission.
Pierluigi suffers from two skin conditions: eczema and dermographism. His mother withdrew him from St Eugene de Mazenod RC primary in Camden, north London, last September after he was told to wear the school uniform rather than the grey corduroys bought from John Lewis school uniform department.
He now attends St Mary's primary in Brent.
Pierluigi's mother, Gabriella Valencia, said headteacher Valerie Robertson refused to believe that flannel trousers inflamed eczema on his legs. His mother said it was so bad he could barely walk.
"It has really knocked his confidence," said Mrs Valencia. "He feels he must have done something wrong because he is not with his friends.
"I would like her (Mrs Robertson) to apologise to him."
Mrs Robertson said: "It was very sad that his mother decided to take him out of school. She did not inform us of his eczema when he joined."
The Disability Discrimination Act was extended to schools from September last year.
The case is being sent to the Special Educational Needs and Disability Tribunal today and is likely to be heard in May.
To win, the commission has to prove that the school's failure to change uniform regulations put Pierluigi at a "substantial disadvantage".