During pre-Columbian times, the region around Santa Rosa was a transition zone between the Lenca tribes, centered farther east and south, and the Chortí Maya, who inhabited the hill country along the Guatemalan border. The remnants of indigenous villages have been discovered at several sites near Santa Rosa, such as El Pinal, Yarushin, and Zorosca.

Early in the colonial period, the Spaniards established a major settlement nearby at Gracias, but Santa Rosa itself was not founded until 1705. Juan García de la Candelaria, a captain of the Gracias town militia, applied for and was granted an encomienda in the name of Santa Rosa de los Llanos, also known as La Sábana. The site was strategically chosen on a hill above a fertile valley, along the royal road between Guatemala City and Gracias; the town quickly prospered as a transport way station and a cattle-ranching area.

A major boost in the nascent town’s fortunes came in 1793, when the Spanish crown chose to move the Royal Tobacco Factory from Gracias to Santa Rosa, as the young town was nearer to the producing regions of the Valle de Copán. Santa Rosa grew steadily after this, with migrants coming from Guatemala and directly from Spain to establish their own small farms and businesses.

In the late colonial period and well into the 20th century, the tobacco industry based in Santa Rosa was by far the most important economic activity in western Honduras, and as a result the city quickly eclipsed Gracias as the most important urban center in the region.

Santa Rosa, along with Comayagua and Tegucigalpa, was deeply involved in the independence wars and the resulting strife between the different Central American republics. Honduran president José Trinidad Cabañas briefly made Santa Rosa the country’s seat of government in 1853, when Honduras was under constant threat from Guatemala. In 1869, when the department of Copán was established, Santa Rosa was designated as its capital.