Saeed, along with Amir Hamza, Abdur Rehman Makki, M. Yahya Aziz and four others filed a plea at the LHC, naming the federal government, Punjab government and the Counter Terrorism Department (CTD) as respondents.
The plea urges the court to declare the First Information Report (FIR) registered against the them null and void. It further adds that Saeed has no relation with the banned Lashkar-e-Taiba (LeT), Al-Qaeda or any other similar organisations.
"The accused are not involved in any any activities against the state. Accusations by the Indian lobby naming Saeed as the mastermind behind Mumbai attacks are not based on reality," the plea said.
Earlier this month, Punjab's CTD, in a major crackdown against terror financing, registered 23 cases against the JuD chief and 12 aides for using five trusts to "funnel funds to terror suspects".
The CTD said it had registered cases under the Anti-Terrorism Act in Lahore, Gujranwala and Multan against the leadership of banned outfits JuD, LeT and Falah-e-Insaniyat Foundation (FIF).
The move follows pressure from the Financial Action Task Force (FATF), which last year placed Pakistan on its "grey list" of countries with inadequate controls over money laundering and terrorism financing.
The watchdog gave Pakistan an October deadline to improve its efforts against terror financing.
The CTD said a large-scale investigation had been launched into the finances of proscribed organisations JuD, LeT and FIF in connection with the implementation of UN sanctions against these designated entities and persons under the directives of the National Security Committee in its meeting on January 1 this year chaired by PM Imran Khan for implementing the National Action Plan.
( With inputs from IANS )