The Indio Station was established prior to 1936. It was primarily intended as a back-up station for the El Centro Sector and also for the purpose of checking all farms and ranches in the Coachella Valley. Entry of the United States into World War II resulted in the Valley playing an important role for food production during this period and severe manpower shortage was alleviated by the use of alien labor, both legal and illegal; therefore, it was imperative that the station concentrate its efforts on checking farms and ranches in the Valley and prevent the departure of illegal aliens who might want to move further north.

With the completion of the All-American Canal system, an abundant water supply transformed the Coachella Valley’s former arid desert area into the extremely productive ranch and farmland it is today, which greatly increased the workload of the station. When control of the border was accomplished during "Operation Wetback", emphasis was then diverted from farm and ranch check to transportation check.

Today, the Indio Border Patrol Station is responsible for patrolling the northern portion of the Imperial County totaling approximately 10,800 square miles.