It didn't take long for the club to gain promotion to the Tokushima Prefectural League 1st division, this occurred in 2006.

From 2016 onwards, the club never again got relegated, and won qualification to the Emperor's Cup as Tokushima representatives every year since then.

[4] FC Tokushima won the 2020 Shikoku Soccer League, giving them the right to participate for their second time in the competition.

However, the 2020 season of the Regional Champions League was cancelled due to the COVID-19 pandemic, then, delaying their second appearance at the competition, which would happen on the 2021.

[6] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.