The 1998–99 Siena Saints men's basketball team represented Siena College in the 1998–99 college basketball season.

This was head coach Paul Hewitt's second season at Siena.

The Saints competed in the Metro Atlantic Athletic Conference (MAAC) and played their home games at Pepsi Arena in Albany, New York.

They won the 1999 MAAC men's basketball tournament to earn the conference's automatic bid to the 1999 NCAA Division I men's basketball tournament.

The Saints received the 13 seed in the West region where they were defeated by No.