[1][2] Used as an outpost for Pardo's expedition into the interior of what was known to the Spaniards as "la Florida", Fort San Juan was the foremost of six forts built and garrisoned by Pardo in modern-day North Carolina, South Carolina, and Tennessee to extend Spain's effective control deeper into the North American continent.

[5][6] In 1566, a fleet under the command of Pedro Menéndez de Avilés established the coastal mission of Santa Elena on what is now Parris Island in South Carolina.

Pardo's expedition set out from Santa Elena in December 1566, and followed the routes of the Congaree and Wateree rivers up to the native city of Cofitachequi, which had been visited 26 years prior by Hernando de Soto.

The expedition continued along the Wateree past where it becomes the Catawba River (in modern-day naming conventions), arriving in 1567 at the Native American city of Joara (spelled "Xuala" in later Spanish maps).

[8] Pardo's expedition was forced to stop at Joara for an extended period of time due to heavy snowfall in the Blue Ridge Mountains, which prevented their progress.

During their two-week stay at Joara, Pardo's men constructed Fort San Juan in the style of a blockhouse, and possibly also built a palisade and moat.

[7] After two weeks at Joara, Pardo left a garrison of 30 Spanish soldiers at the newly built fort under the command of Hernando Moyano de Morales.