Japanese Super Cup
The year 1999 was marked with S-Pulse's first appearance in the Japanese Super Cup, replacing Yokohama Flügels after their merger with Yokohama Marinos. However, S-Pulse lost the match 2–1. After performing well in both league stages, S-Pulse were up against local rivals Júbilo Iwata in the title decider, and after a 3–3 aggregate draw, lost the tie 4–2 on penalties. The new millennium brought better results for S-Pulse. Victory in the Asian Cup Winners' Cup in 2000 and victory in the final of the Emperor's Cup in 2001 meant that the S-Pulse trophy cabinet was beginning to fill up, and victories in the 2001 and 2002 Japanese Super Cups meant that the club had won four cups in three years.