[1] It is a tributary of the larger Wawa River with headwaters located in the mountain boundaries of Sibagat and the Province of Surigao del Sur.

The Boguko River got its name from the native word bagako, which means "mysterious".

Variant forms and spelling of Bagako or in other native languages exist such as Bagoko and its present name Boguko.

The Boguko River headwaters originate from the Diwata Mountain Range of Barangays Banagbanag and New Tubigon where its mouth located in Barangay Magsaysay joins with the larger Wawa River.

[3] In early years, a logging company operating on that area constructed an access road and built a highly elevated detour bridge that crossed the Boguko River and they named it "Boguko Bridge".