The 1998–99 season was Kilmarnock's first season in the newly formed Scottish Premier League.

Kilmarnock finished fourth in the Scottish Premier League with 56 points.

They reached the fourth round of the League Cup, losing to Airdrieonians.

[1] Kilmarnock also reached the third round of the Scottish Cup, losing to rivals Ayr United[2] and lost in the second qualifying round of the UEFA Cup to Sigma Olomouc.

[3] Kilmarnock's score comes first Win Draw Loss Postponed