On the verge on bankruptcy in 1979, they were denied a license for the following season and were sent down to the. The team survived just one season at the highest level in the Bundesliga. Bundesliga Nord and in 1977, they finally advanced to the top flight as winners of their division. Pauli was part of the new second-tier professional circuit in the 2.

The success of the Bundesliga, and the growth of professional football in West Germany, led to the formation of the in 1974. Division championships in 19, and runner-up finishes in 19, were each followed by promotion-round play-off disappointment. They took their next Regionalliga Nord title in 1966 and, while they performed far better in the play-offs, still failed to advance to the top-flight, losing out to on goal difference, having conceded two more goals. Pauli won their division in 1964, but finished bottom of their group in the promotion play-off round. Nearly a decade-and-a-half of frustration followed. Pauli found themselves in the second-tier Regionalliga Nord. Hamburger SV, Werder Bremen, and joined the new circuit as the top-finishers from the Oberliga Nord, while St. Promotion to the Bundesliga In 1963, the – West Germany's new top-flight professional league – was formed. Pauli were overtaken by rivals such as and, but finished fourth a number of times.

In the late 1950s and into the early 1960s, St. The club continued to play well throughout the early 1950s, but were unable to overtake rivals, finishing in second place in five of the next seven seasons, and going out in the early rounds in each of their championship-round appearances from 1949 to 1951.

They advanced as far as the semi-finals, where they were knocked out 2–3 by eventual champions. Pauli to its first appearance in the national championship rounds. A second-place finish in the 1947–48 season led St. Historical chart of St Pauli league performance after WWII After the war, the club resumed play in the in 1947.

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