Police said a fight broke out at Linnéskolan in Malmö on Wednesday evening, involving a 17-year-old boy and at least four other people.
The boy died after having his throat slit, though police refused to comment on what type of weapon was used. A pile of bloody clothing was also found at the scene.
"We have interrogated many people and it's pretty clear how it happened, but it's nothing we want to get into right now," Bo Paulsson of the Malmö police told news agency TT.
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The 16-year-old was arrested at 6am Thursday morning. The police will continue interrogating witnesses throughout the day.