In 1942, following their victory over the Dutch, the Japanese occupied Bangka as part of the Pacific Theater of World War II. To support their military operations against the Allied forces and strengthen the island's defenses, they constructed an airstrip to serve as a base for their aircraft. Initially, the airstrip was not intended for commercial or civilian flights; rather, it functioned as a strategic military installation designed to protect against potential Allied attacks. During the war, the Japanese constructed bunkers and other fortifications around the airport for defense and to stockpile weapons. Some of these structures can still be seen today.

After Indonesia gained independence, the airport began operating commercial flights and was subsequently renamed Pangkalpinang Airfield (Indonesian: Pelabuhan Udara Pangkalpinang). In 1985, the status of Pangkalpinang Airfield was upgraded to an airport (Indonesian: Bandara). In 1999, the airport was renamed to its current name in honor of Depati Amir, a Bangka aristocrat and national hero of Indonesia who resisted Dutch colonialism and the exploitation of resources in Bangka during the 19th century.

In 2007, the management of the airport was transferred from the Directorate General of Civil Aviation of the Ministry of Transportation to Angkasa Pura II, which has since been rebranded as InJourney Airports.

A new terminal, located to the northeast of the old terminal across the runway, was inaugurated by President Joko Widodo on 14 March 2019. After its opening, all airport operations were relocated to the new terminal, and the old terminal was abandoned, gradually falling into disrepair. Although there have been proposals to repurpose the old terminal as a bus terminal, these plans have yet to be realized.

To attract international tourists to Bangka, plans are underway to designate the airport as an international airport, enabling the launch of international flights. Relevant infrastructure is currently being developed to accommodate these flights, with the goal of achieving international status by 2026.