In 1538 San Juan del Norte was under Spanish domain, Rodrigo Contreras was the Spanish representative appointed as governor. During this period, an important part of Nicaraguan territory was what is now present day San Juan de Norte. San Juan's name originates from of the expeditions of the San Juan river or “Desaguadero” by the Spanish explorers Machuca de Suazo and Calero.
In 1796 while under Spanish domination, San Juan experienced economic and commercial growth due to what was called Free Port. Giving San Juan the same rights and privileges that the ports of Omoa in Honduras and Saint Thomas of Castille in Guatemala enjoyed during the same period of time. Nevertheless, the free port privileges of San Juan's port did not last for long. The peoples of the Mosquito and Zambo tribes of the Nicaraguan Atlantic Coast took control of the entrance to the San Juan river blocking the Spanish ships that arrived in the bay from sailing up the San Juan river.
In 1839, the same year the Panama canal was opened, King Mosco ruler of the Miskitos, on the Atlantic Coast, granted Britain the right to explore the vast expanse of forest that covered the territory of San Juan. This opened the way for Great Britain to set its sights on the construction of an interoceanic channel to cross the Nicaraguan territory via the San Juan River and the southern part of what is now Lake Nicaragua.
In February 1848 the English army occupied the old San Juan port entrance to the proposed interoceanic channel. Prior to this, King Mosco had changed the name of San Juan to Greytown in honor of the then governor of Jamaica Sir Charles Grey. Greytown began a free port with a governor and diplomatic representatives from other countries.
On July 13, 1854 San Juan was destroyed by the US Navy war frigate Cyane in retaliation for the injury of the US Minister Slon Borland. The Minister was injured in a riot that ensued after a Nicaraguan in a canoe was killed when struck by the US ship Routh on March 15th, 1854. Among those aboard was the Minister who tried to intervene and was over come by the angry crowd before the San Juan police arrived to arrest the captain. On July 11, 1854 the US demanded that Nicaragua make economic reparations within 24 hours or they would take action against the port city. By November 1860, San Juan was rebuilt and became one of the most important commercial centers in the area.
Historic legacy can currently be found near the city of San Juan
del Norte. There were five cemeteries built around 1860 by the settlers
of San Juan, each for a different group of settlers. There you will
find an English, a Spanish, a Mormon, an American and a Nicaraguan
In 1983 San Juan del Norte became another causality to the destruction of Nicaragua's civil war years. At that time, most of San Juan's population emigrated to Costa Rica , the rest resettled in Managua, Granada and Bluefields. In 1990 an effort was undertaken to begin the reconstruction of San Juan del Norte by 30 repatriated families and 20 families of ex- militia.