The Baton Rouge station was first established during the late 1920's. At the time, the primary responsibility of the station was apprehension of alien crewman deserters, domiciled aliens, and aliens being smuggled into the United States by boat. The station was under the general supervision of a Border Patrol supervisor in the New Orleans District office. Appointed officers did not receive any formal instruction and "on the job training" was the primary means to increase officer efficiency.

Due to economic necessity during the Great Depression, the station was closed as an economic move. When World War II began, the station was again temporarily opened. The primary duties during this time consisted of vehicular traffic checks, checking hitchhikers, public transportation checks, and general "backup station" for New Orleans. The main concern of the stations in the area was the prevention of enemy agents from entering the country. At the end of the war, operations ceased as the need for the station diminished.

In 1958, the station in Baton Rouge was re-established. Foreign flag shipping activity at the Port of Baton Rouge had increased considerably, and alien crewmen deserters were leaving the area undetected. These crewmen were successfully entering the country and taking northerly or easterly routes out of Baton Rouge, because these routes did not pass through any Border Patrol station.