British-born Islamic militant Ahmed Omar Saeed Sheikh and three co-defendants have denied the kidnap and murder of Wall Street Journal reporter Daniel Pearl.
Journalists and members of the public are still not allowed inside the proceedings, but a source from inside the makeshift courtroom in the Karachi Central Jail reported the development.
It had been uncertain if Saeed would enter a plea, because he had previously said he did not recognise Pakistan's "British" secular court system and demanded to be tried by an Islamic court.
The trial began under tight security in the jail where Saeed and the three others are held on charges of murder, kidnapping and terrorism. They face the death penalty if convicted.
Police snipers manned positions in guard towers and on top of buildings as the judge and prosecutors arrived shortly before the proceedings began.
Some 70 additional officers have been added to guard the jail throughout the trial because there are fears that cohorts of the suspects "might try to free them or even kill them," said Amanullah Niazi, deputy superintendent of police at the Karachi jail.