The Karachi-based anti-corruption court issued warrants after Federal Investigation Agency reportedly found evidence that Gilani and his minister Faheem were involved in the Trade Development Authority of Pakistan corruption
The FIA submitted a charge sheet, giving evidence to Judge Mohammad Azeem to approve the non-bailable warrants.
The court previously issued legal notices to both Gilani and Faheem but neither had responded.
Gilani and Fahim have been accused of involvement in the seven-billion-rupee freight subsidy financial scam in TDAP.
The key accused, Muhammad Firdous, turned approver against the former prime minister and the ex-minister.
The hearing of the case was adjourned to June 17.