Due to the ongoing Second World War Sweden focused more on military readiness in case of an invasion than on sport, this led to Halmstads BK being forced to use 29 different players during the season and the result came thereafter as the club ended up in 3rd place behind Malmö BI and winners IS Halmia. Halmstads BK was the superior team in 1941 Division 2 but failed to defeat GAIS in the qualify for Division 1. Halmstads BK won Division 2 after hard competition with local rivals IS Halmia in 1942 and in the qualify the club was able to defeat Lundby IF with 3–2. The club ended up in 6th place in 1943, only 1 point from earning a medal. Halmstad was close to fall out of the top division in 1944 but a series of victories saved them in the end. 1945 saw the club end up in 8th place. In 1946 the club ended up second from last after a poor season, however the club's youth squad won the unofficial youth championship, first defeating IFK Göteborg and then playing 4–4 against AIK in the final, winning on drawing the winning lot, in the youth squad there were players like Sylve Bengtsson, Gunnar Johansson, Olle Ericsson, Östen Ståhl and Åke Hallström, who all later became noted players in the club's history. Halmstads BK returned to Division 1 after only 1 season in Division 2, the club crushed Örgryte IS with 6–1 in the 1947 qualify, the team also played their first match outside Sweden this year, they defeated Helsingør IF with 8–2 and the youth squad won the youth championship again after defeating Djurgårdens IF with 2–1. Just like the year before Halmstads BK time in Division 1 only became 1 year as they ended up dead last in 1948. In 1949 Kalmar FF proved too strong and Halmstads BK ended up in 3rd place in the league, the club also refused to participate in the district championship as a protest to the "unsporting behavior" the district association had showed the club the previous year.