In 1993 the fast moving, faster hitting Subagja won men's doubles at the then biennial IBF World Championships in Birmingham, England with fellow countryman Rudy Gunawan.

However, Subagja's regular partner for most of the 90s was another fellow countryman, the equally fast and hard-hitting Rexy Mainaky, and they formed the most successful team of the decade.

Subagja and Mainaky won more than thirty international titles together, including all of badminton's major championships at least once.

They captured Olympic gold at Atlanta in 1996, the IBF World Championships in 1995 at Lausanne, Switzerland (a repeat title for Subagja), and the prestigious All-England Championships back to back in 1995 and 1996.

Subagja and Mainaky were bronze medalists at the 1997 IBF World Championships in Glasgow, Scotland.