The club was formed by a merger of Prins Hendrik (1 April 1906; Prince Henry) and Ende Desespereert Nimmer (1904; And Never Despair).

In 1977, PEC Zwolle reached the finals of the KNVB Cup, losing to Twente in extra time, and missed out on promotion to the Eredivisie by one point.

The money for this came from the Slavenburg's bank, which was led by FC Zwolle chairman Jan Willem van der Wal.

Eibrink brought legendary players like Piet Schrijvers, Johnny Rep and Cees van Kooten to the club.

In 1985, PEC Zwolle '82 were relegated to the Dutch first division, largely due to an injury-ridden main squad.

Despite a promising start to the 1988–89 season, the club finished in 16th place, which meant that it was relegated to the First Division.

The players' wages could not be paid, and a debt to the Slavenburg's bank appeared which had been overseen by the board for around ten years.

After the bankruptcy, it was decided that the club had to sever all ties with the troubled finances of the past and make a fresh start.

The first years of the 'new' club were hard, but after 1992–93, a new team filled with talents such as Jaap Stam (who would later play for PSV, Manchester United, Lazio, Milan and Ajax), Bert Konterman (Feyenoord and Rangers), Johan Hansma (Heerenveen) and Henri van der Vegt (Udinese) played attractive and successful football.

In the KNVB Cup, FC Zwolle reached the quarter-finals, losing to Feyenoord in a penalty shootout.

After many failed attempts in the play-offs, FC Zwolle finally managed to secure a return to the Eredivisie by winning the First Division in 2002.

They lost 7–1 away at Feyenoord, while their rivals Vitesse and Volendam managed to beat their opponents Utrecht and RBC Roosendaal.

At the beginning of the 2004–05 season, FC Zwolle was considered one of the favourites for the title in the First Division, along with Sparta Rotterdam.

The 2005–06 season started well, with FC Zwolle fighting for the league's top spot in the first months.

Spijkerman's assistant trainer Harry Sinkgraven finished the season, leading the club to the play-offs, in which Eredivisie side Willem II proved too strong.

During the 2010–11 season, FC Zwolle held the top spot for a long time, but had to leave the title to RKC Waalwijk.

Shortly after winning the championship of the Eerste Divisie, the club announced that the name will be changed to PEC Zwolle again.

[4] In 2014, under the guidance of new head coach Ron Jans, PEC Zwolle earned their first major silverware by winning the KNVB Cup, beating league champions Ajax 5–1 in the final.

[5] On 3 August 2014, PEC Zwolle also won the 2014 Johan Cruijff Schaal (Dutch Supercup) by defeating AFC Ajax, this time by 1–0.

However, following the winter break, Zwolle experienced the complete opposite of what it had before; it lost all matches and eventually ended at the 9th place in 2018.

On 3 March 2023, Zwolle gained a 13–0 win over FC Den Bosch in a league game, as the team broke a broad series of records in the process.

[16][18] PEC player Lennart Thy claimed the top goalscorer's award in the Eerste Divisie for the season, having scored 23 goals in 36 appearances.

[19] Zwolle won immediate promotion back to the Eredivisie at the end of the season, finishing second in the league table.

The first goal scored in the new stadium was by FC Zwolle player Bram van Polen, coming on 22 August 2008 against Cambuur.

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

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

The following players were called up to represent their national teams in international football and received caps during their tenure with PEC Zwolle: