[1] During most of the 1980s, the recently merged club competed in the third-tier Oberliga Westfalen, where they counted among the leading teams but never achieved promotion.

The team lost to Eintracht Braunschweig and Fortuna Düsseldorf, but secured a place in the newly formed third-tier of the German football pyramid, the Regionalliga West/Südwest.

Except for a brief stint in the fourth tier, Paderborn enjoyed moderate success with regular trips to the DFB Pokal.

The team's advance into professional football brought with it a professionalisation of its structures, and, in 2005, construction began on a new 15,000-seat stadium, which replaced the dated Hermann-Löns-Stadion.

The team started well; in the fourth game of the campaign against Hannover 96, midfielder Moritz Stoppelkamp scored a volley from 83 metres out, headline a Bundesliga record for the furthest ever goal.

[7] Upon relegation, a number of key players such as Alban Meha, Mario Vrančić, Lukas Rupp, Marvin Ducksch and captain Uwe Hünemeier left the club, while coach Breitenreiter joined Schalke.

Starting the 2015–16 season with Markus Gellhaus in charge, Paderborn surprisingly gave former Germany international Stefan Effenberg his first coaching job in October 2015.

After Steffen Baumgart took over as coach in April, the team picked up 11 points from his five games in charge, but could not escape the relegation zone, finishing in 18th position.

That should have been a third relegation in a row, this time to the non-professional Regionalliga West, but Paderborn were unexpectedly saved by 1860 Munich not receiving a license to play in the 3.

In 2019, a remarkable turn of events, the newly promoted side completed another top-two finish, which returned Paderborn to the Bundesliga after years of turbulence.