Tokushima Vortis traces its roots to 1955, when pharmaceutical giant Otsuka founded a company football team in Tokushima, the capital of Tokushima Prefecture on the island of Shikoku. For decades the club competed as a corporate side, reaching the old Japan Soccer League Division 2 in 1989 but remaining outside the professional pyramid due to the parent company's cautious approach to commercialisation.
The club's identity crystallised in the mid-1990s around the "Vortis" name, a coinage drawn from the Italian word "Vortice" meaning whirlpool — a nod to the famous Naruto whirlpools that churn through the strait just off the Tokushima coast. After back-to-back JFL championships in 2003 and 2004, Tokushima Vortis entered the J.League in 2005 as a fully professional club. Early seasons were uneven, including back-to-back last-place finishes in 2007 and 2008, but a patient rebuild under coach Minobu Naohiko gradually lifted the club up the J2 table.
The defining moment in the club's history came in 2013, when Tokushima won the J2 promotion playoff, defeating Kyoto Sanga in the final at the National Stadium to become the first professional Shikoku club ever to compete in Japan's top division. Their sole J1 season in 2014 ended in relegation, but the milestone stood. A second promotion followed in 2020 under Ricardo Rodríguez, this time as J2 champions — the club's only league title to date — before another single-season spell in J1 in 2021.
Back in J2, Tokushima remains the standard-bearer for football on Shikoku, still backed by Otsuka and its Pocari Sweat brand, playing home matches at Pocari Sweat Stadium in Naruto.