Kazi Abdul Hasib Md Sayeed, 45, had arrived at that house at Mollaparha four days ago.
His family brought his dead body to Chittagong Medical College and Hospital (CMCH) on Tuesday afternoon and claimed the man committed suicide.
Police said there were ligature marks on Sayeed's throat, but he suffered a major wound on his head too.
Three people - Sajida Ahmed Mishu, Lucky Aktar and Imran Ahmed – have been arrested over the incident.
Mishu claimed to police that she was Sayeed's wife, and Lucky was her mother and Imran brother.
CMCH police outpost's Nayek Pankaj told bdnews24.com that Mishu and Lucky brought in Sayeed's corpse around 6pm.
"They said the judge had committed suicide. Duty doctors said he died long before he was brought to the hospital."
Later, Imran was arrested at the house at Mollaparha, Chittagong Metropolitan Police’s Additional Deputy Commissioner (West) SM Tanvir Arafat said.
Chittagong Medical College and Hospital police post Sub-Inspector Zahirul Islam said Sayeed’s second wife and her relatives took him to the hospital in the afternoon, but doctors there said he had been brought dead.
He said Sayeed married for the second time three months ago in Chittagong.
"There is a wound on his head. There are also ligature marks on his throat. An autopsy will be done."
The arrestees were yet to be questioned, he said, adding that he had nothing else to share at this point.
Before being promoted to the Naogaon court, Kazi Sayeed worked as the joint district judge on Patia in Chittagong.