On 31 August 1941 in the first league game against SC Juventus Zürich their striker Alex Mathys scored seven goals as Basel won by 10–1.
The fourth round was another home tie and they beat the higher tier Nationalliga team BSC Young Boys by three goals to nil.
The next round gave Basel another home tie against 1st League team Solothurn and they completed an easy victory, winning 6–1.
However, despite this defeat, with the following 3–0 away game victory against their direct opponents Luzern, who also playing at risk of relegation near the bottom of the table, and a 2–0 home game victory against their other direct opponents Nordstern, Basel ended the season with 18 points in 13th position, just two points above local rivals Nordstern, who ended the season on the relegation spot.
In the Swiss Cup Basel started in the 4th principal round with a home tie at the Landhof against lower tier local side FC Pratteln.
Two goals from Numa Monnard and one from Roger Courtois during the last five minutes of the match meant that Basel lost the game 0–3 and Lausanne won the national double.
[9] In the Swiss Cup Basel started in the 3rd principal round with an away tie against lower tier local side FC Allschwil and a 6–0 victory.
[10] In the Swiss Cup Basel started in the 3rd principal round with an away tie against lower tier local side SC Schöftland this ended with a 5–1 victory.
After his playing career the Austrian ex-international Anton Schall, who suffered from a rare heart condition, moved to Switzerland and took over Basel as club trainer for the 1946–47 season.
There were fourteen teams contesting in the 1946–47 Nationalliga A. Basel finished their season in fourth position in the table, with twelve victories from 26 games, scoring in total 60 goals.
Anton Schall was to continue as first team manager, but he died at the age of 40 years, during a workout on the football field, shortly after the pre-season training had begun.
[23] Basel started in the 3rd principal round of the Swiss Cup on 4 November 1951 with a home game against lower tier Wettingen and won 7–0.
They were drawn away against lower tier local team FC Riehen, but the match was played at the Landhof and Basel won 6–0.
But because at the beginning of the previous season they had lost important players, such as goalkeeper Gianfranco de Taddeo to Cantonal Neuchatel, midfielder Kurt Maurer to La Chaux-de-Fonds and striker Walter Bielser to Biel-Bienne, the Basel board of directors were changing their approach to the subject.
They were drawn away against lower tier local team SC Binningen, but because they waived the home advantage the match was played at the Landhof and Basel won 5–0.
Bruno Michaud returned from Lausanne-Sport, Fredy Kehrli, Jean-Jacques Maurer and Charles Turin were hired from Biel-Bienne who had suffered relegation the previous season.
Then, despite two high wins, 5–0 away against Lausanne-Sport and 6–1 at home against Bellinzona, the afore mentioned three defeats against Young Boys, Zürich and Grasshopper Club caused the change in manager position.
Hermann Suter, who had played 16 seasons for Basel and in 229 league and cup games had scored 104 goals, ended his active football career.
In the next round Basel were drawn at home at the Landhof against lower tier team FC Porrentruy and this ended with a 5–2 victory.
Despite an early 1–0 lead and in total 18–0 corners, Werner Decker and Heinz Wirz each scored for the under dogs who had a very young Karl Odermatt in their team.
14,000 spectators paid their entrance tickets to see the game, much needed money because the club was suffering under a bad financial situation at that time.
An interesting point to note was the contact that was made between the club's chairman, Ernst Weber, and the scorer of the final goal of the match, Benthaus.
Not only these two players left the squad, but also Paul Speidel moved on to Cantonal Neuchatel and Josef Hügi (Hugi II) was nearly at the end of his football career.
Basel finished the championship in sixth position with twenty six points, with ten wins and six draws from 26 matches, scoring 59 goals conceding 51.
[45] In the Swiss Cup Basel started in the 3rd principal round, on 3 November, with a 4–0 home win, in the St. Jakob Stadium against Black Stars.
The Wankdorf Stadium hosted the Swiss Cup Final on 15 April and Basel played against favorites Grasshopper Club Zürich.
Two goals after half time, one by Heinz Blumer and the second from Otto Ludwig gave Basel a 2–0 victory and their third Cup win in their history.
This saw them visit British Hong Kong, Malaysia, Singapore, Australia, New Zealand, French Polynesia, Mexico and the United States.
First team manager Jiří Sobotka together with 16 players and 15 members of staff, supporters and journalists participated in this world tour from 10 January to 10 February 1964.
[50] Fourteen teams contested the 1964–65 Nationalliga A. Basel ended the championship with eleven wins and five draws in their 26 matches, and finished in eighth position with 27 points.