In 1538, the current municipality of San Juan del Norte was under Spanish rule. Its representative was Mr. Rodrigo Contreras. At that time the territory was an important part of his current position with the name of San Juan, which come from one of the boats of the expedition of Captains Machuca Suazo and Calero, explorers “Desaguadero” (Rio San Juan).

During the Spanish domination SAN JUAN is well-known for its commercial prosperity, which unable it in the year 1796 to be called Free Port, with the same privileges they enjoyed at that time Omoa ports in Honduras and Santo Tomás de Castilla Guatemala.

However, the privileges of Free Port of San Juan did not last long, Miskitos and Zambos, Indians of the Nicaraguan Atlantic Coast took the mouth of the Rio San Juan, to block the Spanish ships that arrived at the bay.

For the year 1839 with the opening of the Panama Canal, on the Atlantic Coast of the Miskito King Mosco, granted Britain the right to logging in large areas of forest that covered the territory of San Juan. This enabled Britain to set their sights to the construction of canal that would cross the territory of Nicaragua via the Rio San Juan.

On January 1, 1848 the British army occupied the old San Juan entrance to the proposed canal. Shortly before King Mosco had changed the name to San Juan to Greytown in honor of the then governor of Jamaica Sri. Charles Grey. In practice, Greytown became a free port with its own local governor and diplomatic representatives in severals countries. On March the 15th of 1854 San Juan was destroyed by the frigate Cyane of the Navy United States. This was caused by the death of a Nicaraguan who was traveling in a canoe, which was caused by the Routh American ship, which traveled the U.S. Minister Mr. Slon Bolrand. Before this event San Juan police wanted to arrest the American ship captain, opposing this, the then Minister Bolrand, which led to contentment in the local population, thus forming a riot where the minister was wounded Bolrand.

Unidos Mister Slon Bolrand .

Before this event, the United States government requested financial compensation much higher than calculated, this financial compensation had to be delivered within 24 hours, and otherwise they would have to destroy the city. Thus, the July the 13th, 1854 the Port of San Juan with about 80 houses was completely destroyed.

On November the 22nd , 1860 the port was again one of the most important commercial centers of the region and by decree of the 20th February 1861 adoption of the regulation achieves quality of Constitution, to contain the political requirements, economic and civil and criminal justice in the city and port of San Juan.

Currently found in the municipality of San Juan del Norte as municipal heritage, five cemeteries that were built by the locals in 1860. Cemeteries are distinguished, an English cemetery, a Spanish man, a Mormon, a native American and a cemetery.

In 1983 San Juan del Norte suffered another destruction due to war time, most of the population migrated to Costa Rica and a minority to Managua, Granada and Bluefields.

In 1990 begins the reconstruction of the new San Juan del Norte with 30 returned families and 20 ex-militiar.