In the 1996–97 season, the team started to climb slightly up the leagues due to various complicated mergers with Jagiellonka and Wisła, causing various name changes such as Jagiellonka/Wisła Włocławek in 1997 for example.

Despite this, as the level of football standard rose so did the attendances, reaching an all-time high of 7000 spectators for the inaugural match of their highest ever league start in I liga in 1997.

The club's fortunes have since improved slightly, winning the regional Polish Cup in 2013.

After finishing the 2022–23 IV liga season as runners-up of the Kuyavia-Pomerania group, Włocłavia withdrew their senior team from competition.

Fierce cross-town rivals Kujawiak Włocławek contest the local derby with them.