Imam Abdul Aziz has been accused of threatening protesters outside the Red Mosque.
|Imam Abdul Aziz|
Last week, Taliban fighters attacked the school in Peshawar, killing 152 people, including 133 children.
Mr Aziz said that the authorities should focus on arresting people accused of more serious crimes.
"My case is very small and even a sub-inspector can grant me bail," he said.
The BBC's Anbarasan Ethirajan says that Mr Aziz is well known for his pro-Taliban views.
Earlier this year, a school run by the cleric renamed its library in honour of the former al-Qaeda leader, Osama Bin Laden.
A spokesman for the Red Mosque said they would resist the arrest of Mr Aziz.
|A man holds a sign during a protest near the Red Mosque in Islamabad|
The demonstrators are also being investigated for holding an unlawful protest.
Pakistan has stepped up its anti-terror operations since the attack on the Army Public School in Peshawar on 16 December.
Earlier this week, the government announced new measures to tackle terrorism, including the establishment of military courts to hear terrorism-related cases.
Prime Minister Nawaz Sharif said on Wednesday that there was a "changed Pakistan" since the tragedy and that there would be "no place for terrorism, extremism, sectarianism and intolerance."
That doesn't sound like Pakistan. Watch your back PM Sharif you are messing with centuries of insanity.