A bench of Justices Dipak Misra and Amitava Roy asked the Bihar government to transfer Shahabuddin to Tihar Jail within a week, saying "it is the obligation and duty of this court to ensure free and fair trial".
The apex court said trial in the cases registered against Shahabuddin will be conducted through video conferencing from Tihar Jail.
"We direct the state of Bihar to transfer Mohammad Shahabuddin from district jail Siwan to Tihar jail Delhi," the bench said.
The petitioners had told the apex court that Shahabuddin should be transferred from Siwan jail to any other jail outside the state for free and fair trial in the cases pending against him.
The Bihar government had earlier told the apex court that it is not "averse" to shifting Shahabuddin from Siwan prison to Tihar Jail here.
The state government had told the apex court that Shahabuddin is facing trial in 45 cases, including one in Jharkhand.