The arrested youth included a college student, the police said, adding a mask and a "green and white flag", an apparent refence to the Pakistani flag, were recovered from them.
On the basis of available evidence, police arrested a "chronic" stone-pelter identified as Tahir Nasrullah, a resident of Parimpora area on the outskirts of Srinagar, a police spokesman said.
He said Nasrullah had recently taken admission in the Government Degree College, Magam, and taking advantage of being new in the area, he resorted to creating disturbances there.
He was identified on the basis of physical features like the kind of clothes he wore, his height, colour of school bag he carried, the spokesman said.
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He said the police team apprehended him outside the college when Nasrullah was changing his clothes from uniform to civil.
The police recovered a mask, college uniform and a mobile phone from his bag, the spokesman said.
His arrest, the spokesman said, led to the arrest of another stone-pelter identified as Samir Bhat, a resident of Yarigund area of Magam.
Further investigation into the matter is going on, he said.
Kashmir has been witnessing recurring incidents of stone-pelting in various parts for the last few months.