The 1998–99 Winthrop Eagles men's basketball team represented Winthrop University during the 1998–99 college basketball season.

This was head coach Gregg Marshall's first season at Winthrop.

The Eagles competed in the Big South Conference and played their home games at Winthrop Coliseum.

They won the 1999 Big South Conference men's basketball tournament to receive the conference's automatic bid to the 1999 NCAA Division I men's basketball tournament – the first appearance in program history.

16 seed in the South region, the Eagles lost to No.