After the Munich air disaster of 6 February 1958, he temporarily took over as manager while Matt Busby recovered from his injuries and, having assembled a substitute team, steered United to the 1958 FA Cup Final. Murphy had not been on the fatal flight because he had been away managing the Welsh team in a World Cup qualifying game. Murphy managed Wales at the 1958 FIFA World Cup in Sweden when they reached the quarter-finals in their only appearance to date in a World Cup finals tournament. They lost 1–0 to Brazil (the eventual winners), to a goal by 17-year-old Pelé.