Casa Pia

Beginning and breakthrough (2014–2021)

Borneo was formed by former Putra Samarinda supporters who were dissatisfied with their team's lack of achievements. PT Nahusam Pratama Indonesia bought Perseba Bangkalan on 7 March 2014, which gave them direct license to compete in the 2014 Liga Indonesia Premier Division, and changed their name to Pusamania Borneo Football Club.

First major honours (2014–2017)

After beating PSGC Ciamis on penalties in the 2014 Liga Indonesia Premier Division semi-finals, they were promoted to the Indonesia Super League. On 27 November 2014, Borneo won their first title by becoming champion of the 2014 Liga Indonesia Premier Division after beating Persiwa Wamena 2–1 in the final.

In the 2017 Piala Presiden, Borneo went on to defeat cup favourites, Persib 5–3 on penalties shootout in the semi-finals thus reaching their first cup final in the club history where Borneo faced off against Arema. However, Borneo suffered a 5–1 defeat to the opponent.

On April 2017, the club changed their name to Borneo Football Club. The club then went on to signed New Zealand national star Shane Smeltz for the 2017 season and then managed to signed former West Ham United and Real Madrid player Julien Faubert ahead of the 2018 season.

Rebuilding project (2022–present)

In 2022, Borneo reached the 2022 Piala Presiden final but slipped away from winning the cup after a narrow 1–0 lost to Arema.

AFF competition debut (2024–2025)

In 2024, Borneo secured top of the table in the 2023–24 Liga 1 regular series with 70 points, but lost 2–4 on aggregate to Madura United in the championship series semi-finals. Nevertheless, Borneo were subsequently given Persija's spot in the 2024–25 ASEAN Club Championship, after the latter, who had qualified as 2022–23 Liga 1 runner-ups, declined to participate. Borneo also reached the 2024 Piala Presiden final facing off against Arema for the third time in the cup final in which again, Borneo lost 4–5 on penalties.

Borneo then competed in the 2024–25 ASEAN Club Championship which is their first official participation in international tournament. The club was then drawn in a group alongside Thai club Buriram United, Singaporean club Lion City Sailors, Malaysian club Kuala Lumpur City, Philippines club Kaya—Iloilo and Vietnamese club Công An Hà Nội. On 22 August 2024, Borneo won 3–0 against Lion City Sailors at home. After the conclusion of the group stage, Borneo manage to finished with 6 points but it wasn't enough to qualified to the knockout stage.

AFC competition debut (2026–present)

Borneo then finished the 2025–26 Indonesia Super League as runners-up which saw the club qualified to the 2026–27 AFC Challenge League and the 2026–27 ASEAN Club Championship. In the AFC Challenge League, Borneo was drawn in Group D alongside Myanmar club Yangon United, Philippines club One Taguig and Taiwanese club Tainan City.