A number of specialized units exist in the Jacksonville Fire and Rescue Department, and several are housed in Special Operations in the Operations Division.

Special Operations is home to the nation's first organized municipal Haz-Mat Unit, a group of firefighters who respond to chemical, biological and radiological incidents.

Florida Task Force 5 Urban Search and Rescue (USAR) is part of the Operations Division. Jacksonville USAR teams have deployed in Florida and other states during hurricanes to help with search and rescue operations. The department's Technical Rescue Team is also part of the USAR unit and Special Operations. This team deals with people trapped in dangerous situations.

Special Operations also has a Marine Unit that operates out of Station 38 and Station 39. This unit fights fires on the water or shore and provides water to engine companies fighting fires near the St. Johns River.

JFRD also has two airport fire stations assigned to Special Operations: Station 16 at Jacksonville International Airport, and Station 56 at the Cecil Commerce Center.