They were first promoted to the old Japan Soccer League Division 2 in 1989, but the company's reluctance to professionalize the team forced it to compete in the former JFL and current JFL. In the 1997 old JFL season, they first sported a Vortis Tokushima name, but the lack of fan interest at the time forced them to go back to the corporate identity. They finally adopted the Tokushima Vortis name for good after winning the new JFL championship in 2004 and being promoted.
The first season in J2 was naturally a difficult one for Vortis, but they surprised many sceptics with their determination and quality of play. The team rose as high as fourth place, at one point, before slipping down the table later in the season to finish ninth. In 2006, the team was forced to rebuild, as the players who took the team into the J.League began to hit the ceiling of their abilities, and made way for younger replacements. As a result, despite the encouragement of a local rivalry with Ehime FC, Tokushima drifted down-table, and they followed it up with a last-place finish in 2007 and 2008.
In 2013 they earned fourth place in J2, matching the same placement they had two years before in the division and twenty years before in the old JFL Division 1; this time they won the playoff, defeating Kyoto Sanga F.C. in the final round at the National Stadium in Tokyo, thus becoming the first professional Shikoku football club to compete in the top division of their national league.
Until their promotion, they were the only former JSL member currently a member of the J. League which has never competed in the top tier of Japanese football. With promotion and the creation of the J. League Division 3 in 2014, the distinction will be taken over by Blaublitz Akita.