The group said that it carried out an attack in a Shia Muslim area of the southern city of Quetta last Saturday which killed almost 90 people.
However, it is not clear whether Mr Ishaq’s detention is directly related to the attack.
Mr Ishaq spent a decade in jail before being released in 2011.
A heavy contingent of police surrounded Mr Ishaq’s residence and held negotiations with him, after which he gave himself over to the police, the BBC‘s M Ilyas Khan reports from Islamabad.
He had been released from jail a few months ago, our correspondent adds.
It is not clear whether Mr Ishaq has been formally charged with any offence. Under public order laws, suspects can be held in Pakistan for three months without any charge.
Pakistani authorities have long been criticised for not taking enough action against groups such as LeJ that foment sectarian violence.
When a local journalist asked Mr Ishaq in 2011 what intended to do after his release from jail, he replied his organisation would continue its “good work” – fighting those who opposed their version of Islam.