The 1998–99 Florida A&M Rattlers men's basketball team represented Florida A&M University during the 1998–99 NCAA Division I men's basketball season.

The Rattlers, led by third-year head coach Mickey Clayton, played their home games at the Teaching Gym as members of the Mid-Eastern Athletic Conference.

They broke through to win four games to capture the MEAC tournament and secure the conference's automatic bid to the NCAA Tournament – the first appearance in school history.

16 seed in the East region, The Rattlers were defeated by No.

1 overall seed and eventual National runner-up Duke, 99–58.