Police said Saddikul Islam Bangla Bhai, chief of the outlawed Jagrata Muslim Janata Bangladesh group, was arrested with his wife at a hideout in the district of Mymensingh on Monday.
Two of Bangla Bhai's associates were also captured.
A militant was killed and an officer of the elite Rapid Action Battalion force suffered a shotgun wound to the head.
Bangla Bhai was also injured, but it was not immediately known how seriously.
His capture comes four days after Shayek Abdur Rahman, another leading fugitive Islamist, was detained in the northeastern town of Sylhet.
Security forces had surrounded Bangla Bahi's hideout since midnight on Sunday and closed in before sunrise.
The militant and his men threw bombs at the security forces and later opened fire, police said.
Shayek Rahman led another outlawed Islamist group, Jamaat-ul-Mujahideen.
Both groups are fighting for the introduction of Islamic law in Bangladesh and are blamed for a wave of bombings, including suicide attacks, that have killed at least 30 people and wounded 150 since last August.