Arrest

After the imposition of emergency and suspension of constitution, Chaudhry constituted an eight-member bench of Supreme Court judges duly headed by himself, and immediately quashed the provisional constitution order, declaration of emergency and the suspension of the constitution, and ordered all civil and military personnel to ignore the order. He also ordered all the chief justices of high courts and judges of the Supreme Court and High Court not to take oath under the PCO. Soon after, on November 3, the Supreme Court was stormed by the 111th brigade of the Pakistan Army and Chaudhry was arrested along with seven other judges. Musharraf replaced Justice Chaudhry with Abdul Hameed Dogar as the de facto chief justice of Pakistan and also administered the oath of office to three other judges of the supreme court under the PCO. Justice Dogar later took a fresh oath on the constitution after it was restored and the PCO withdrawn.

Chaudhry's house was sealed and he was allowed limited visitors and no one met him officially until the new Prime Minister Yousaf Raza Gillani ordered to uplift the house arrest on his first day of premiership. However, he continued to denounce Musharraf's declaration of emergency and vowed to push for a return to the rule of law.
On 15 November Geo News reported that Chaudhry had ordered the Islamabad Inspector General of Police to take action against his and his family’s house arrest and their possible removal to Quetta. According to the channel, Chaudhry held the interior secretary, the commissioner, the deputy commissioner and the assistant commissioner responsible for his house arrest. He said he was still the Chief Justice of Pakistan and the official residence was his by right.

On 18 November in a letter to prominent English-language newspaper The News he wrote: "I will fight till the last drop of my blood to save the Constitution of Pakistan and so will resist any move to deport me to some far-flung area with the intention to separate me from the lawyers and the Pakistani citizens".

In February 2008, Chaudhry wrote an open letter to President Musharraf from house arrest.