Before there was a fort, there was a road. In November 1846, Major Philip St. George Cooke and the Mormon Battalion camped three miles north of the future fort site, beginning their historic mission to build a wagon road from the Rio Grande to California. Brigadier General Stephen Kearny had tasked them with proving a route to the Pacific, and this stretch of river marked where their road would turn southwest toward the copper mines of Santa Rita and eventually to Alta California. Cooke's camp sat across the river from the settlement of San Diego, 258 miles southwest of Santa Fe. The road they blazed became known as Cooke's Wagon Road, and it transformed this bend in the Rio Grande into a crossroads of continental significance.

Captain Israel B. Richardson established the post on December 24, 1853, initially calling it Cantonment Garland after General John Garland, commander of the Ninth Military District. The name soon changed to Fort Thorn, honoring 1st Lieutenant Herman Thorn of the 2nd U.S. Infantry, who had drowned in the Colorado River in 1849 while serving as Garland's aide. Richardson brought his garrison of 3rd U.S. Infantry from the recently abandoned Fort Webster, building adobe walls around the new post and placing only the hospital outside the enclosure. A 3.5-mile acequia channeled water from the Rio Grande to irrigate farms and power a sawmill. The fort anchored the defense against Apache raiders who terrorized settlers and travelers along the El Camino Real.

Assistant Surgeon T. Charlton Henry described the problem with clinical precision in his 1856 Sanitary Report. Standing pools formed during river overflows and persisted through the fall months. Cottonwood trees once shaded these pools, but soldiers had cut most of the timber for construction and firewood, leaving the stagnant water exposed. Henry blamed "the miasma" for the fevers, not understanding that mosquitoes breeding in those pools carried the disease. Report after report documented the garrison's debility. By 1859, the accumulation of sickness and complaint finally closed the fort. The soldiers marched away, leaving their adobe walls to the elements and the settlement of Santa Barbara nearby to its fate.

Abandonment did not mean the end. When the Civil War split the nation, Fort Thorn found new purpose. On September 26, 1861, Union cavalry from the Regiment of Mounted Rifles clashed with Bethel Coopwood's Confederate horsemen at a site fifteen miles upriver, the Skirmish near Fort Thorn adding the post's name to Civil War records. Confederate General Henry Hopkins Sibley subsequently used the fort as an assembly point for his ambitious invasion of northern New Mexico, gathering his forces before marching up the Rio Grande. After the Confederate campaign collapsed, the California Column occupied Fort Thorn in July 1862, using it as a staging point before crossing the flooded river to reclaim Mesilla and Franklin, Texas.

The final abandonment came not with a battle but with a newspaper notice. On October 25, 1860, the Mesilla Times reported that Navajos had raided Fort Thorn, driving off livestock and killing an ox. Apaches pursued the raiders and recovered the property, but the damage was done. The forty settlers remaining near the fort "apprehending a renewal of hostilities, have abandoned the place and come into the Mesilla valley for security." They brought several thousand head of stock with them. "The settlement is consequently entirely broken up," the newspaper concluded. Fort Thorn appeared on survey maps through 1861, its military reservation carefully outlined, but the land itself held only ghosts. The 1950 film Two Flags West later depicted the fort, giving Hollywood's version of life on this forgotten frontier.