Sagan Tosu was founded in February 1997 in Tosu, Saga Prefecture, rising from the ashes of Tosu Futures, a predecessor club that had collapsed due to insolvency. The revival was driven by community support — more than 50,000 signatures were gathered calling for a new club — and this grassroots spirit has defined the club's identity ever since. The club name reflects that ethos: "Sagan" evokes sandstone (砂岩), the idea of countless small grains binding together to form something solid and resilient.
The early years in the Japan Football League and then the newly formed J2 League from 1999 were marked by financial turbulence and near-extinction on multiple occasions, but the club survived each crisis and gradually built stability. That perseverance paid off when, at the end of the 2011 season, Sagan Tosu earned promotion to the J1 League for the first time, thirteen years after joining the J2 as one of its founding ten members.
Their J1 debut in 2012 confounded expectations: rather than being relegated immediately, they finished fifth, posting the best home record in the division that season. Two years later, in 2014, the club reached the summit of J1 for the first time across multiple matchweeks, with a genuine title challenge before finishing fifth again. That era also brought notable international partnerships and the signing of Fernando Torres in 2018, which raised the club's global profile. A 13-year spell in the top flight ended with relegation in October 2024, and the club returned to J2 in 2025.