The city of Panevėžys has a long history of football in Lithuania. Until 2014, the city was represented by 7-time title winners FK Ekranas. However, FK Ekranas was unable to meet financial criteria to participate in 2015 season and lost eligibility to participate in the A Lyga. The club was declared bankrupt. To fill the void, FK Panevėžys was established at the beginning of 2015, right before the new season start. The club made its debut in the I Lyga (second tier), finishing its first season in the eighth place. In 2016, the club improved its performance and finished in the fifth position.
In 2017, Panevėžys aimed to win the I Lyga and return a club from the city of Panevėžys to the A Lyga. However, the start of season was disastrous, which resulted in the resignation of the head coach Virginijus Liubšys. Eventually, the club finished 10th in the league table. In the 2018 season under new coach Alexandru Curteian, FK Panevėžys achieved their goal of winning the I Lyga and achieved promotion to the A Lyga for the first time in history. They finished their first season in the top flight (2019 A Lyga) in 5th position.
Former Lithuanian national team coach Valdas Urbonas took over the club for the 2022 season. After a successful start to the season, Panevėžys was in first place in the table after 14 matches played. After a series of weak performances, the club dropped to third place, leading to the dismissal of Urbonas in September 2022. Urbonas was replaced by Italian national Gino Lettieri. At the end of the 2023 season, Panevėžys secured the first place in the league, 12 points ahead of second place team FK Žalgiris, becoming Lithuanian champion for the first time in history.