FIFA 99 features an elite league called the "European Dream League" in which 20 top teams from across Europe battle it out in a league format. It was also the first game to feature a block containing teams which did not pertain to any of the main leagues (back then, it was known as "Rest of Europe" since all teams were European, the vast majority of them featured either in the 1998-99 season of the UEFA Cup or Champions League).

Graphically, it is a major improvement over FIFA '98, with the inclusion of basic facial animations and different players' heights as well as certain other cosmetic features such as improved kits and emblems, although they are unlicensed. Gamers may also create their own custom cups and leagues and select the teams they wish to participate.