Tavria was one of its founders and eventually became the very first Ukrainian champion in 1992, under the Simferopol born manager Anatoliy Zayaev, defeating FC Dynamo Kyiv, Ukraine's most successful club in the final, held in Lviv.

More players from that era were Oleksandr Holovko, a defender who also played many years for Ukraine national team, and captain Serhiy Yakovych Shevchenko, who scored the championship goal against Dynamo Kyiv.

Having earned the right to participate in 1992–93 UEFA Champions League, Tavryia were knocked out in the first round by Swiss club FC Sion.

The Russian Sport-Express posted an article (No.3 (43), 25 January 2000, page 9) stating that the Ukrainian champions Tavria were threatened by the Football Federation of Ukraine to compete at the CIS Cup in 1993.

After the annexation of Crimea by Russia, Tavriya asked permission from UEFA and FIFA to shift to the Russian league next season.

On 18 June 2015, the Football Federation of Ukraine executive committee voted in favor of re-establishing the club now to be located in Kherson (the largest Ukrainian city bordering Crimea).

Prior to the start of the 2020–21 Ukrainian Second League the club merged with FC Tavriya Novotroitske, but continued to play under its original name.

[5][6] On 28 March 2022 Tavriya ceased club activities after 2022 Russian invasion of Ukraine and subsequent temporary occupation of Kherson Oblast.