The Camilo Jose Cela School in Madrid suspended the schoolgirl, identified as Najwa Malha, as she refused to remove her hijab despite being told that the headscarf was in violation of the school dress code.
While the school released a statement explaining its move saying that the its internal regulations bar 'the use of hats and any other article of clothing that cover the head", the girl has alleged discrimination.
"I feel totally discriminated against," Malha told The Telegraph.
The girl, born to Moroccan parents, said that she decided to wear the scarf despite her mother warning against it.
Association of Moroccan Workers and Immigrants in Spain has slammed the school's decision saying that it violated Malha's right to a basic education guaranteed by the constitution.
This is not the first time such an incident has been reported from Spain. In Nov 2009, a Muslim lawyer was asked to leave the court as she refused to remove her headscarf.
Countries across the world such as France and Canada have also raised objections to the headscarves burqas worn by Muslim women citing security reasons.