District Judge I.S. Mehta framed against Malik the additional charge under Section 121 (waging war against the country) of the Indian Penal Code (IPC) in an in-chamber hearing.
Malik has also been charged under Sections 121A, 122 and 123 of the IPC.
The high court had earlier asked the trial court to frame charges against Malik under Section 121, section 121-A (conspiracy to commit war against the state), Section 122 (collecting arms with intention of waging war against the government) and Section 123 (concealing with intent to facilitate design to wage war).
The high court directions came Dec 3 last year on the National Investigation Agency's (NIA) plea challenging the trial court's Sep 4 order refusing to frame charges against Malik for waging war against the government.
The trial court had dropped against Malik the charges dealing with waging war against the government, conspiracy and collecting arms to wage a war against the country.
After the special court Wednesday framed additional charges against Malik, he pleaded not guilty and claimed trial. The court fixed April 1 for recording of evidence.
Recording of evidence will begin with the examination of co-accused-turned-approver Amir Abbas Dev. The NIA arrested Dev for his alleged role in the case but he later turned approver and was granted pardon by the court.
Fifteen people were killed and 79 others injured in the Sep 7, 2011 blast outside gate number five of the Delhi High Court complex.
The NIA said that the terror attack was plotted with an aim to get the death sentence of 2001 parliament attack convict Afzal Guru commuted to life term. Guru was executed Feb 9.