In 1768, the Jesuit missions in Leyte were assigned to the Augustinians until 1804 when some of the parishes were ceded to the secular clergy and the others (those on the eastern coast of Leyte, Biliran, which was given to the diocesan clergy) to the Franciscans.

During the Second World War, the Japanese Imperial Forces landed at Barrio Pinamopo-an in the Municipality of Capoocan, Leyte. A few days later the islands of Leyte and Biliran were occupied by the enemy. When the American and Filipino troops surrendered in 1942, many civilians and members of the armed forces in Leyte fled to the hills in order to engage in guerrilla warfare. Biliran Island was under the control of the 1st Battalion commanded by Captain Antonio Cinco.

The island is originally known as Panamao where it was then under the jurisdiction of Leyte. On April 8, 1959, Republic Act 2141 created the Province of Biliran. The law was later amended by Republic Act No. 5977, enacted on June 21, 1969, and by Republic Act No. 6415, approved on October 4, 1971, it became a regular province.