Partapur police station in-charge Dinesh Sharma said Jani was arrested from the Delhi-Doon highway near Partapur bypass when he was on his way to Dehradun from the capital last night.
Banners calling for boycott of Kashmiris and asking them to leave Uttar Pradesh had been put up by the organisation on NH-58 outside the colleges where students from the Valley study.
The outfit had said it was only the first step and it would launch a "halla bol" campaign from April 30 to "banish" the Kashmiris who do not leave the state on their own.
Yesterday, through his advocate, the organisation's chief submitted a surrender application before the special CJM court.
Upon being questioned, he told police that he had got the hoardings put up because soldiers were being martyred in Kashmir.
Jani had first shot into the limelight in 2012 when he damaged a statue of former chief minister Mayawati. Last year, he had been arrested for threatening to kill JNU Students Union president Kanhaiya Kumar and Umar Khalid.