Asif Zaheer, Nadeem, Sarmad Siddiqui were produced in the Karachi ATC amid tight security. All the three suspects pleaded not guilty to the charges against them.
The court has summoned all witnesses in the case for the next hearing scheduled for March 14.
The trio were arrested by the Counter Terrorism Department of the Sindh police in October for providing financial and logistical support to the attackers.
On June 8, about 10 Taliban militants disguised as police guards stormed the Jinnah airport premises and opened fire with machine guns and a rocket launcher, triggering an all- night-long gun-battle with Pakistani security forces.
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The outlawed Tehreek-e-Taliban Pakistan (TTP) claimed responsibility for what was the first large-scale terrorist attack at the country's largest airport in years.
TTP chief Mullah Fazlullah and former spokesperson Shahidullah Shahid are among eight others declared proclaimed offenders in the case.
Following the attack, the Pakistani military launched a campaign of aerial strikes on militant hideouts in the tribal areas along the Afghan border.
The volatile tribal region is considered the nerve centre of the Taliban.
The attack's mastermind Abu Abdul Rehman Al Maani was killed in overnight airstrikes by Pakistani forces in North Waziristan last year.
The IMU, an outfit consisting of militants mostly from the central Asian Uzbek state, had claimed that its suicide bombers carried out the attack in alliance with the TTP.