Known as the world’s third-largest island, Borneo spans approximately 730,000 square kilometers and is governed by three nations: Malaysia (Sabah and Sarawak), Brunei, and Indonesia (Kalimantan). While similar regional basketball events had been held in earlier years, it wasn’t until 1999—following a friendly match in Brunei organized by the Kota Kinabalu Basketball Association (KKBA)—that the Borneo Cup Basketball Championship was officially established through the collective agreement of various regional clubs. The Brunei (Bandar Seri Begawan Amateur Basketball Association) stepped up to host the inaugural event, which tipped off from June 25 to 27, 1999, at Chung Hwa Middle School under the title “1st Borneo Men’s Basketball Invitational Tournament”

Unlike the current format, the first year featured only a Men’s Open category. The hosts, Brunei, fielded their national team as preparation for the SEA Games, while Kota Kinabalu (KK), Miri, and Labuan all sent representative teams, collectively marking this historic milestone.

The KK delegation was led by then-KKBA Chairman Wong Yu Len as Chef de Mission, with Vun Yun Hin as Head Coach, So Su Kiong as Team Manager, and Teo Lip Cing as Secretary. The roster included Wan Wing Hang, Lim Lee Keong, Wong Yuen Ming, Voo Vui Chung, Tan Teck Khoon, Yong Vui Kong, Tan Ming Gan, Lo Hin Siong, Soo Yuet Wing, Tee Nguk Hung, Herbert, and Oliver.

After three days of intense competition, a powerful Miri side emerged as the inaugural champions with an undefeated record, defeating Brunei (78–67), KK (71–56), and Labuan (80–68). Labuan also put on a strong showing to finish as runners-up (beating KK 79–56 and Brunei 78–72), while Brunei secured third place with a narrow 67–62 victory over KK.

During the tournament, representatives reached a consensus for KK to take over the hosting duties for the second edition the following year (2000). Under the diligent preparation of the KKBA, the 2nd Championship was held at the KK Community Hall from June 15 to 17, 2000, with Yap Chee Ming serving as Organizing Chairman and Chong Lip Cheng as Secretary. This edition also saw the unanimous introduction of the Men’s Veteran Invitational category.

Miri continued their dominance by successfully defending the Men’s title, while Brunei claimed the first-ever Veteran’s crown. The Women’s category was eventually introduced during the 5th edition in Brunei in 2003, with the hosts taking the inaugural title.