Because the addition of '94 Kyo Kusanagi in the previous game was well received by fans, Kyo's character from The King of Fighters '95 was added to the roster as another alternate version of Kyo.

The "Japan Street" stage is based on a viaduct next to Esaka Train Station and SNK's headquarters, in Osaka.

Since this game did not have a storyline, the staff decided to have Rugal Bernstein as the boss character noting that "he's the only character who truly represents the ultimate KOF boss." Additionally, some of his special moves were redesigned, which the staff found to have made him the strongest version of Rugal as well as one of their favorite boss characters in the series.

In the Japanese version of The King of Fighters: Dream Match 1999, King throws a glass of wine at the screen during the intro cutscene.
Along with this, both King and Ralf Jones' entrance poses show them drinking alcohol.
These references to alcohol were censored in other versions.