Juan de Ugarte (1662–1730) was a Jesuit missionary-explorer in Baja California Sur, Mexico, and the successor to Juan María de Salvatierra as head of the peninsula's missions.
Ugarte was born in Tegucigalpa, Honduras. His younger brother, Pedro de Ugarte, was also a Jesuit missionary in Baja California.
Juan de Ugarte was initially the procurador for the newly established California missions in 1697–1700. As such, he was stationed in Mexico City, administering the Pious Fund of private donations that supported the missions and seeing to the logistical support necessary to sustain them.
In 1701, Ugarte went to the peninsula as its third missionary, following in the footsteps of Salvatierra and Francisco María Piccolo. First at Loreto and then at San Javier (1702–1730), among the Cochimí Indians, Ugarte was an able and energetic leader in the expansion and development of the mission system. He served as visitador or superior for the missions in Salvatierra's absence and after the latter's death in 1717.
Ugarte led several expeditions of overland exploratio to seek out mission or visita sites in the region surrounding San Javier. More spectacularly, he oversaw the construction of a ship, "El Triunfo de la Cruz", from locally harvested lumber called Gueribo found at La Sierra "La Giganta". In September 1720, Ugarte sailed his new ship from Loreto to La Paz to help found a new mission there. In the following year, he sailed to the head of the Gulf of California, trying to resolve the longstanding question of whether California was an island or a peninsula.