The team was originally run by the company S-Lap Communications, with funding from the citizens and Shizuoka Television.
S-Pulse is a combination of the S from Shizuoka, Shimizu, and Soccer, and Pulse from English to mean the spirit of all those who support the team.
A previous representative of the city in the old Japan Soccer League had been Nippon Light Metal S.C., who was a co-founder of the Second Division and competed in it for three seasons (being renamed Hagoromo Club in 1973 and relegated as such in 1974, to fold in the Tokai League in 1975).
S-Pulse also took part in the 72nd Emperor's Cup but their run was ended by Yokohama Marinos in the quarter-finals.
After finishing top of Group B they defeated Gamba Osaka in the semi-finals only to lose in the final once again to Verdy Kawasaki.
After finishing top in their group, S-Pulse made it to the final, defeating Bellmare Hiratsuka 5–0 in the semi-finals.
1997 and 1998 saw further improvements in the league; S-Pulse narrowly missed out on a 1st-place finish in the first stage of 1998 on goal difference.
However, they failed to win any more silverware, coming closest in the 1998 Emperor's Cup with a 2–1 defeat in the final to Yokohama Flügels.
The title deciding matches saw S-Pulse take on their local rivals, Júbilo Iwata.
The great season was capped off by two good cup runs, both ending with defeat in the quarter-finals.
They closed the year with a run to the Emperor's Cup final in which they did not concede a single goal.
League Cup ended at the group stage after they only managed to pick up 8 points.
After finishing the league season on a high, S-Pulse went on to reach the quarter-finals of the Emperor's Cup but their run ended with defeat at the hands of Kashima Antlers.