In 1943, they again won their division – now called the Gauliga Westmark – and advanced through the playoff rounds to the national final where they were defeated 0–3 by Dresdner SC.

During the latter years of World War II from 1943 to 1945, the club played as part of the combined wartime side Kriegsspielgemeinschaft Saarbrücken with SC Altenkessel.

After the war, the occupying Allied authorities dissolved most organizations within Germany, including sports and football clubs, as part of the process of de-Nazification.

In sport, this was manifested as separate 1952 Olympic and 1954 FIFA World Cup teams for Saarland and the establishment of a short-lived football league for the state called the Ehrenliga.

FC Saarbrücken was one of a number of sides forced out of German football, but unlike other clubs, they did not play in the puppet league.

They won the division but were refused promotion or further participation, mainly due to the resistance of other clubs, among them Strasbourg, which had been forced to play in German competition during World War II.

They organized a tournament in 1949–50 called the Internationaler Saarlandpokal ("International Saarland Cup") that had them play 15 home matches against teams from Austria, Denmark, France, Sweden, Switzerland and Yugoslavia.

The top three sides then joined hosts Saarbrücken in a playoff round, which the home team eventually won in a 4–0 victory over Stade Rennais UC of France.

The tournament was abandoned for 1952 as an agreement was reached to allow teams from the Saarland re-admission to the German Football Association (DFB).

This episode in the history of German football would play itself out with the odd appearance of a separate side from Saarland in the 1954 World Cup preliminary rounds.

Saarbrücken would also make an appearance in the 1955–56 European Cup as Saarland's representative and were eliminated by Milan in the first round, despite a 4–3 win at the San Siro in the first leg.

Sixteen teams were selected to play in the new league based on their performance, financial health and a geographical distribution intended to fairly represent all parts of the country.

Saarbrücken's selection to the new league was arguably the most controversial as the club's recent record was not as strong as their divisional rivals Neunkirchen, FK Pirmasens and Wormatia Worms.

The belief is that their advantage lay in the fact the club had a long association with Hermann Neuberger, an extremely influential figure in German football – and a member of the selection committee.

The club was relegated to the second tier Regionalliga Südwest where they finished strongly in each of the next three seasons, but were unable to advance through the Bundesliga promotion rounds.

Another poor showing in 2006–07 saw the club in 15th and relegated again, this time to the fourth division Oberliga Südwest, where they narrowly missed out on Regionalliga promotion in 2007–08.

On 3 March 2020, they became the first team from the fourth tier in the history of the DFB-Pokal to reach the semi-final, after beating Fortuna Düsseldorf in the quarter-final.

FC Saarbrücken Amateure until 2005 during the times the senior side played in professional football, first made an appearance in the Ehrenliga Saarland from 1948 to 1951.