San Juan lies on the east portion of the Municipality. It is bounded on the north by Barangay Isaub, on the east by Sulu Sea, on the west by Barangay Iraan, on the south by Barangay Tagpait and on the southwest by Barangays of Poblacion and Iraan River. It is two (2) kilometers away from the Poblacion and a 10 to 15-minute walking distance.

 Barangay San Juan is named in honor of Saint John. according to Juana Hugo, a religious woman, the creek found in this Barangay reminds her of Saint John who baptized Jesus. She believed that San Juan would be a good name of the place.

 From that time on, the resident called their district as Barangay San Juan.