During the latter year, the sports club dissolved its football department and FC Universitatea Craiova took its berth in the top flight.

Generally considered the same entity with the old club, FC U continued its tradition for the next two decades, but was reorganised several times and retroactively deemed an unofficial successor.

To the same degree with CS U, FC U claims all the trophies and records of the original club, but according to court orders, its only major honour would be the 1992–93 Cupa României.

In 1991, Universitatea Craiova conquered its last national title and Romanian Cup, under the management of Sorin Cârțu.

[11] In April 2014 the High Court of Cassation and Justice confirmed that the Romanian Football Federation "acted in accordance with regulations and statutes in force when members voted to exclude the club".

[24] In 2017, Adrian Mititelu created a new company and his team was allowed to participate in the top regional tier of Dolj County.

The team were leading the table by 13 point from the second place with 13 wins, 3 draws and 0 defeats but the season was interrupted on 9 March 2020, after 16 rounds, due to COVID-19 pandemic.

On 11 May 2020, the Romanian Football Federation announced that the season was discontinued and the best-ranked teams from each series (after 16 rounds) were promoted to Liga II.

He left with a high profile win against Bucharest rivals Rapid București, only to be replaced by Dan Vasilică who was the caretaker for the team until Ovidiu Stîngă was appointed.

Ultimately U Craiova reached the play-offs of the competition and got the promotion to Liga 1 after a draw against FK Miercurea Ciuc, and later secured the title after a win over Rapid.

This promotion meant that after a lot of ups and downs over the last 10 years, U Craiova 1948 got in to the first tier of Romanian football for the first time since 2011.

Also brought as a coach was a former national for Romania with a joint record of 35 goals (alongside Gheorghe Hagi) Adrian Mutu.

Napoli revitalized the entire squad but being to far away from the play-offs at the time of his spell Craiova went to the play-out round of the competition and managed to achieve the goal of avoiding relegation finishing on the 10th place.

In the European play-offs Craiova beat in semi-finals FC Voluntari only to lose to CFR Cluj in the final after a very close match, with some refereeing mistakes.

His departure led to the brief return of Nicolo Napoli, marking his tenth term at the helm, which lasted for four matches before being succeeded by Eugen Trică.

Despite these changes, the team was unable to secure its position in Liga 1, culminating in relegation after a three-year stint in the top flight.

Many ultras groups exist, but in 2013 a strong division among the fans occurred due to the uncertainty regarding the true identities of the two clubs which claim the record of Universitatea.

In March 2018, FC U Craiova supporters attending a friendly game between Romania and Sweden at the Stadionul Ion Oblemenco booed CS U player Alexandru Mitriță upon being substituted out.

They also broke chairs, and as a response CS U fans symbolically used insecticide to "get rid of the stench" left over by Peluza Sud 97 ultras.

On 10 July 2023, the Timișoara Court of Appeal established that the historical record achieved until the end of 1990–91 season belongs to CS U Craiova.