During the operation, particular attention was to be devoted to searching suspected locations of the political and military elements of the Central Office of South Vietnam. A thorough interrogation of all persons apprehended was to be conducted.

During Phase II, II Field Force elements would focus their attention on the eastern portion of War Zone C, conducting search and destroy operations against COSVN, Viet Cong, and North Vietnamese forces and installations. The Saigon River was to be bridged at its intersection with Route 246 west of An Loc. At that site a Special Forces and Civilian Irregular Defense Group camp with an airstrip for C-130's was to be built.

In Phase III, Junction City would be reduced to a brigade-size operation in the vicinity of Tay Ninh city in the southern portion of War Zone C. The operational control for this phase would be passed from II Field Force to the 25th Infantry Division.

Operation JUNCTION City would demonstrate the ability of American forces to enter areas which had been Viet Cong sanctuaries to conduct successful search and destroy missions and construct facilities in these strongholds. In addition, in the weeks forthcoming each of the four enemy regiments under the 9th Viet Cong Division would be met and defeated.