Firefighters put down the blaze at the plant's oil and gas processing unit shortly after midnight and rescuers later discovered one body inside the facility, said Brod's mayor, Ilija Jovicic on Wednesday. Of the nine people injured, four were in serious condition.
Previous reports said eight people were injured in the blast.
Jovicic said the refinery has continued to operate since the explosion, adding that an investigation which was still underway should establish the cause of the explosion.
The Brod refinery, which processes 1.2 million tonnes of crude a year, is majority owned by Russia's Neftegazinkor, a unit of state-owned oil company Zarubezhneft.
Auditors have previously warned that it may face liquidity problems after it piled up losses and its liabilities exceeded assets. The company, however, has dismissed those claims.
A resident of nearby Slavonski Brod, just across the border in Croatia, have complained about rising pollution levels from the refinery for years and Bosnian and Croatian authorities have been working to combat this issue.
Air quality measures showed no major spike in pollution levels on Wednesday, Jovicic said.
Officials from Croatia and Russia, including the head of Zarubezhneft, met on Wednesday in Slavonski Brod to talk about providing gas from Croatia to the Brod refinery, in an effort to reduce air pollution.
"I believe that by the end of 2019 we could have the Brod refinery operating on gas supply from Croatia. At the moment we're working on defining commercial terms of the arrangement," Croatia's Energy Minister Tomislav Coric said after the meeting.