The Arabic language channel al-Alam said Abdolmalek Rigi is being held in eastern Iran.
But the channel gave few other details.
Rigi is said to be behind a series of deadly bombings and killings in Iran´s Sistan-Baluchistan province.
Last October, 42 people, including six commaders of the Revolutionary Guard, were killed in a suicide bombing in Zahedan.
Jundullah was founded in 2002 to defend the Baluchi minority in the lawless region of south-east Iran.
The group has been using neighbouring Pakistan as a base.
In the past, Iranians have accused Pakistan of allowing them to operate there.
Rigi has claimed that the group does not seek to break away from Iran.
He says violence is necessary to draw attention to discrimination in the Islamic Republic.