The 1999–2000 season was Kilmarnock's second season in the Scottish Premier League.

Kilmarnock finished ninth in the Scottish Premier League with 37 points.

They reached the semi–final of the League Cup, losing to Celtic.

[1] Kilmarnock also reached the third round of the Scottish Cup, losing to Alloa Athletic[2] and lost in the first round of the UEFA Cup to 1.

Kilmarnock's score comes first Win Draw Loss Postponed