In 2013, twelve years after being established, FC Botoșani became the first team from its county to be promoted to the top tier of the Romanian league system.

After the war ended, the team was successively named Flamura Roșie, Textila and Unirea, and played mostly in the regional championship and the third division (Divizia C) without significant performances.

[citation needed] One of the most famous Romanian players, Nicolae Dobrin, ended his career at CS Botoșani.

FC Botoșani made their debut in Liga I on 21 July 2013, in a 0–0 draw against CFR Cluj, with eight newcomers in a top tier level of the starting eleven and played most of the match with nine-man as Ciprian Dinu received a red card in the ninth minute.

[5] The next matchday, on 26 July, saw FC Botoșani netting their first Liga I victory, in a 2–1 away win over Gaz Metan Mediaș.

However, after this record, Botoșani had a poor run and manager Cristian Popovici was sacked, letting the team on the 12th place, two points above relegation.

[7] FC Botoșani started the next season with two important victories against Astra Giurgiu and Dinamo București, teams that fought for the championship title.

In the second leg in Georgia, FC Botoșani netted their first European victory in a 3–1 win over Spartaki Tskhinvali to advance to the next round, where they met Legia Warsaw.

[2] After their first qualification in the championship play-offs, FC Botoșani finished the 2019–20 season on the 4th place, thus achieving their best Liga I performance and, once again, qualifying for UEFA Europa League after 5 years since their last participation.

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