Named president of Ford in 1945, Henry Ford II served in that capacity until November 9, 1960, when he resigned and became Chief Executive Officer of the company. During this time, he recognized his inexperience and hired several seasoned executives to support him. On July 13, 1960 he was additionally elected Chairman; he resigned as Chief Executive Officer on October 1, 1979, and as Chairman in 1980. His nephew, William Clay Ford, Jr. would later assume these positions after 20 years of non-Ford family management of the company. During the interim, the family interests were represented on the board by William Clay Ford, Sr., Henry's younger brother.

When his father Edsel, the president of Ford, passed away in 1943, Henry Ford II was serving in the Navy during World War II, and was thus unable to take over the presidency of the family-owned business. The elderly and ailing Henry Ford, company founder, therefore stepped in and served as president until the end of the war. During this period the company began to decline, losing over $10 million a month. President Franklin Roosevelt had been considering a corporate bailout of the company in order to ensure continued war production.

Henry Ford II took over the presidency of the company on September 21, 1945. Since it had been assumed that Edsel Ford would continue in his capacity as president of the company for much longer than turned out to actually be the case, Henry Ford II had received little grooming for the position, and took over the company during a chaotic period—its European factories had suffered a great deal of damage during the war, and domestic sales were also on the decline.

Henry Ford II immediately adopted an aggressive management style. One of his first acts as company president was to fire Harry Bennett, head of the Ford Service Department, who had originally been hired by Henry Ford to stifle attempts at unionization. Next, he hired former General Motors executives Ernest Breech and Lewis Crusoe away from the Bendix Corporation. Breech was to serve in the coming years as Ford II's business mentor, and the Breech-Crusoe team would form the core of Ford's business expertise, offering much-needed experience.

Additionally, Ford II hired ten young up-and-comers, known as the "whiz kids". These ten, gleaned from an Army Air Forces statistical team, Ford II envisioned as giving the company the ability to innovate and stay current with the times. Two of them, Arjay Miller and Robert McNamara, would go on to serve as president of Ford themselves. As a team, the "whiz kids" are probably best remembered as the design team for the 1949 Ford, which they took from concept to production in nineteen months, and which re-established Ford as a formidable automotive company. It was reported that 100,000 orders for this car were taken the day it was introduced to the market.

Ford II's mercurial management style caused the company's fortunes to fluctuate in more ways than one. For example, his offering of public stock in 1956 raised $650 million for the company, but the "experimental car" program instituted during his tenure, the Edsel, lost the company almost half that. Likewise, Ford II hired the creative Lee Iacocca, designer of the Ford Mustang, in 1964, but fired Iacocca due to personal disputes in 1978. Nevertheless, Henry Ford II's overall influence on the company was substantial—by the time he retired as Chairman in 1980, Ford Motor Company was the fourth-largest industrial corporation in the world. He died in Detroit at the age of 70.