Known as the "Football Professor" because of his attention to detail and also as “Napoleon” because of his diminutive 1.61 meter stature, Cramer began his career at Viktoria Dortmund and Germania Wiesbaden. The beginning of his managerial career lead him to clubs such as Teutonia Lippstadt, VfL Geseke, FC Paderborn, and TuS Eving-Lindenhorst. At the turn of the year 1948–49, Cramer found himself in the service of the German Football Association (DFB) for the first time. Until 1963 he served with the designation as Head Coach for Western Germany under the DFB in Duisburg.
Little known, Cramer attempted to make the jump into a career in journalism at this point. He became lead editor for sports for German television station ZDF. Feeling largely isolated from the football world, Cramer decided to call it quits after only six months on the job. Afterward he was sent by the DFB to Japan to serve as a football instructor.
In order to strengthen its national team ahead of the Tokyo Olympic Games four years later, the Japan Football Association had the idea in 1960 of bringing in a foreign professional coach. Cramer was ultimately selected for this role. Through Cramer's coaching and leadership, and the efforts of his players, the Japanese national team achieved a surprise upset of Argentina at the Tokyo Olympics. The significance of this historic result was not lost on Cramer who saw it as a confirmation that Japanese football was vastly improving. Cramer's efforts were not limited to the national team, as he also formulated and implemented policies for general development. The foundation of a first national league, the training of other coaches, and the strengthening of the national team would all contribute to Japan's success at the Mexico City Olympics four years later, where Japan would take home the bronze medal.
On 1 January 1964, Cramer returned to Germany to take up a position as an assistant to German national coach Helmut Schön. In this capacity he was a part of the coaching staff at the World Cup in 1966, where West Germany lost in the final to England. His talents were highly regarded by FIFA (Federation Internationale de Football Association), which contracted him as a coach from 1967 to 1974 and sent him on a tour of the globe, but during this time, Cramer would also run the 1st FIFA Coaching Course in Japan in 1969, and sowed the seeds for a coach training structure in Japan. Additionally, on 1 August 1974, Cramer was selected by the United States Soccer Federation to become the head coach of the United States men's national football team.
During his time in national team service, Cramer received numerous coaching offers from German clubs in the Bundesliga, although he consistently turned them down. Then, on 16 January 1975, he took over the reins as manager of German giants FC Bayern Munich. At the beginning, Cramer faced heavy criticism in Munich, mostly because of his passive management style. With rumors of a sacking swirling around Cramer, he was strongly backed by team captain Franz Beckenbauer, who felt indebted to him because of his insistence that Beckenbauer be allowed to return to the German national team after initially being banned for impregnating a girl out of wedlock.
Cramer would lead Bayern to victory in the 1975 and 1976 European Champions Cup in addition to capturing the World Club Cup in ’76. However, the ’76 Bundesliga season saw Bayern unable to recapture their form, and after a season that saw them fail to defend their domestic title, Cramer was forced to resign his position. Cramer was involved in a trade between Bayern and Eintracht Frankfurt, which saw him take the top spot at Frankfurt, while Frankfurt coach Gyula Lorant made his way to Bayern. Neither club was happy with the trade, as Bayern finished a club worst 12th in the table, while Frankfurt's results were mediocre at best. As a result, the club parted ways with him on 30 June 1978.
Not until the 1982–83 season did Cramer find himself employed in the Bundesliga again, this time with club Bayer Leverkusen. At Leverkusen he managed to lead the club to their first top 9 finish in the league during his second year in charge. Failure to build on that accomplishment lead to his dismissal after his third season in charge.
Never to coach in the Bundesliga again, Cramer instead found coaching positions with various international clubs and associations around the world. In 2002, Cramer officially announced his retirement from football. In 2005, he was inducted into the Japan Football Hall of Fame.