The modern-day Gifu club was founded in 2001 (Seino's last manager Masayuki Katsuno was among the founders, and a former Seino player, Takashi Umeda, recently returned to town and joined the club following a decade-long stint with Oita Trinita). The club was promoted to the new Japan Football League in 2007 after beating Honda Lock S.C. in the promotion/relegation play-offs.
The team earned third place at the end of the 2007 season, meaning it qualified for promotion to J. League Division 2. On December 3, 2007, J. League approved a promotion for the team for the 2008 season.
The team's crest was designed to represent Gifu Prefecture. The top of the crest represents the mountain ranges of the northern part of the prefecture. The flowers are Chinese milk vetch, which are the prefectural flower. Each of the three lines represents one of the Kiso Three Rivers flowing through the prefecture. The banner at the base of the crest is the same as the symbol on the helmet of the victorious Tokugawa clan at the Battle of Sekigahara in 1600.