She transported a Japanese diplomatic mission of 180 people during the first leg of their trip to the Vatican as envoys to Pope Paul V, headed by Hasekura Tsunenaga and accompanied by the Spanish friar Luis Sotelo.
San Juan Bautista was built in 1613 by Date Masamune, the daimyō of Sendai in northern Japan, in Tsuki-No-Ura harbour (Ishinomaki, Miyagi Prefecture).
San Juan Bautista is reported to have required 45 days' work, with the participation of technical experts from the Bakufu, 800 shipwrights, 700 smiths, and 3000 carpenters.
These efforts were seen with disapproval by the Spanish government in Manila, and Los Rios Coronel suggested that Luis Sotelo should not be allowed into Japan any further (C. R. Boxer).
A group of Franciscans led by Father Diego de Santa Catalina, sent as a religious embassy to Tokugawa Ieyasu also sailed on the ship.
The ship is currently on display in a theme park in Ishinomaki, in northern Japan, close to the location where she was originally built.
Assistance had come from a British Columbia lumber company who supplied the massive logs to create masts that had been damaged in the tsunami.