According to the London-based conflict monitor Syrian Human Rights Observatory (SOHR), the man was arrested along with 20 other people in the Tartus province, in western Syria.
The man was the head of the country's military field court from 2011 to 2014, according to Diab Serriya, who is a co-founder of the organization working for inmates at Saydnaya prison.
The now-arrested man was later promoted and was responsible for the military judiciary nationwide – and sentenced "thousands of people" to death.
On Wednesday, 17 people were killed in the Tartus province when clashes broke out between forces loyal to the country's new government and Assad-loyal men. According to SOHR, the clashes erupted when security forces tried to arrest the prison chief.
The clashes in Tartus – a region where many members of Assad's Alawite minority live – broke out when residents refused to let their homes be searched by security forces.
Saydnaya prison, described by Amnesty International as a "human slaughterhouse", has become a symbol of al-Assad's brutal rule. Tens of thousands of political prisoners are said to have been executed in extrajudicial mass hangings and thousands are believed to have died as a result of starvation, torture, and lack of care.
After the fall of the Assad regime, thousands of prisoners were released from the prison.