Japanese Super Cup
1999 began with S-Pulse's first appearance in the Japanese Super Cup, replacing Yokohama Flügels (Flügels merged with Yokohama Marinos at the end of the 1998 season). However, S-Pulse lost the match 2–1. S-Pulse finished 3rd in the first stage of the league and then went on to win the second stage. The title deciding matches saw S-Pulse take on their local rivals, Júbilo Iwata. After a 2–1 defeat and then a 2–1 victory, S-Pulse lost the tie 4–2 on penalties. The great season was capped off by two good cup runs, both ending with defeat in the quarter finals.