The diocese was erected in 1967, through Pope Paul VI, separating from the Diocese of Surigao. The territory of the Diocese of Butuan contained the Province of Agusan del Sur (now the Diocese of Prosperidad) and Agusan del Norte, and Carmelo Dominador Morelos was its first bishop. The diocese is a suffragan of the Archdiocese of Cagayan de Oro.
Vert, on a bend sinister wavy Azure a lily Argent slipped proper, between two pomegranates Or seeded Gules.
The pomegranates allude to Butuan, a Malayan word meaning "full of seeds". It is also a symbol of the Resurrection of Our Lord. The blue wavy bend sinister represents the Agusan River. The green field symbolizes fertility, a promise, and a hope for material and spiritual progress and prosperity in the Diocese. The lily is the symbol of St. Joseph, the Patron Saint of Butuan and titular of the Diocese of Butuan.
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