By some accounts of US analysts at the time, such a headquarters was believed to be almost a "mini-Pentagon", complete with typists, file cabinets, and staff workers with a large guard force.

After the end of the war, the actual headquarters was revealed by VC archives to be a small and mobile group of people, often sheltering in ad hoc facilities and at one point escaping an errant bombing by some hundreds of meters.

[7]: 121 At first, the operations appeared to be succeeding, objectives were reached without encountering great resistance and on 23 February, the mechanized 11th ACR and the 2nd Brigade, 25th Infantry Division, the "hammer" of armor struck against the '"anvil" of the infantry and airborne positioned north and west, giving the VC forces seemingly no chance to escape.

[10]: 198  The VC, highly mobile and elusive, with information sources deep in the South Vietnamese bureaucracy, had already moved their headquarters to Cambodia and launched several attacks to inflict losses and wear down the Americans.

According to calculations by the American command, the VC 9th Division was seriously weakened by the operations, suffering the loss of 2,728 killed, 34 captured men and 139 deserters.

Allied intelligence later learned that, as a result of the operation, the VC moved most of their main force units across the border into Cambodia, rather than stationing them in South Vietnam where they were more vulnerable to attack.

The mobile headquarters had quickly retreated to Cambodia, maintaining its operations and confounding the hopes of the US strategic planners.

Despite the tactical results, Junction City on an operational level didn't accomplish the most important objective, and failed to yield any long-term strategic leverage.