Although no specific references to Cannon Branch Fort have yet been found in historical documentation, it appears likely that the fortification was built by Union troops, circa 1863-1864, as part of a series of forts sited along the railroad to defend supply lines. Once the town of Warrenton, Virginia, was secured by Union forces in April 1863, Major General Joseph Hooker began to use the Orange and Alexandria Railroad as a major supply route for his army.
In July and August 1863, regiments from Pennsylvania and New York, among other northern states, reached the Manassas area as they followed Confederate troops south after the Battle of Gettysburg. These regiments remained in the region until April 1864, to guard the Orange and Alexandria Railroad from additional cavalry and guerilla raids and the fortifications continued to be manned by Union soldiers until late 1864.