The history of Bayugan City traces back to a small settlement inhabited by indigenous communities, particularly the Manobo people, long before formal colonization. The name “Bayugan” is believed to have originated from a native term referring to a path or trail used by early settlers and traders who passed through the area. Over time, migrants from nearby provinces and regions came to the fertile lands of Bayugan, attracted by its rich soil, abundant water sources, and promising opportunities for agriculture and trade.

During the mid-20th century, Bayugan experienced rapid population growth as settlers from different parts of Mindanao and the Visayas moved into the area. This growth eventually led to its establishment as a municipality on August 14, 1961, through Republic Act No. 3017. As a municipality, Bayugan steadily developed its agricultural economy, becoming known for rice production and other crops that supported the livelihoods of its residents.

With continuous progress in infrastructure, commerce, and public services, Bayugan eventually achieved cityhood on June 21, 2007 under Republic Act No. 9405. Today, Bayugan City stands as one of the key urban centers of Agusan del Sur, known not only for its agricultural productivity but also for its growing tourism potential, cultural diversity, and commitment to sustainable development.