حُدثت المباريات التي لعبت في 7 November 1999. مصدر: Japan Football League قواعد التصنيف: 1) النقاط; 2) فارق الأهداف; 3) عدد الأهداف المسجلة. (C) بطل; (P) Promoted. ملاحظات:
^ ابجOccupied one of the top three places at the end of the first part of the season (9th week) and were seeded for كأس إمبراطور اليابان 1999. These clubs were automatically qualified for the tournament, while each of other JFL clubs had to go through the prefectural qualifier. Yokohama F.C. and Kokushikan University were not eligible to be seeded.
^Though Mito HollyHock haven't finished within top two, their promotion was unanimously accepted by the special J. League Board decision. The fact that championship has been won by associate JFL members, Yokohama F.C., was taken into account.
