All-Star Baseball 99 is the first handheld entry in the All-Star Baseball series and differs from its N64 counterpart.

The game features six different modes: exhibition games, a full season (either all 162 games of the 1998 season or various shortened runs), the '97 playoffs, the '97 All-Star game as well as the Home Run Derby, and a batting practice mode. In season and playoff mode, progress is saved via passwords.

On the field, players will control pitching, fielding and batting (bunts and swings are possible). The game also allows players to set team lineups and positions.

The game includes all 30 MLB teams of the 1998 season, including the '98 expansion teams Arizona and Tampa Bay.