Charles Everett Koop was born on October 14, 1916, in Brooklyn, New York. A descendant of Dutch and German immigrants, he was born the only child of John Everett, a banker and business manager, and Helen Apel Koop. Growing up in a three-story brick house in South Brooklyn, he was surrounded by his family, which included his paternal grandparents, and his maternal grandparents, aunts, uncles, and cousins who lived nearby. As a child, Koop seemed out of place at his public elementary and middle schools, which were located in predominantly Italian, Polish, and Jewish neighborhoods. Aside from playing stick-ball and sandlot baseball, and ice-skating in Prospect Park, he enjoyed his time with his close-knit family. His relationships with his family were the primary influence in molding his character and values.

As a young child, Koop enjoyed working with his hands, a trait that he may have inherited from both of his grandfathers, one of whom was an amateur engraver. He was fascinated by medical instruments, and his family nurtured his aspiration to become a surgeon. "The idea of using my mind, then my hands, to heal someone simply fascinated me," he remembered. Koop developed the manual dexterity required of a surgeon by using each hand interchangeably to tie knots or to cut out pictures from magazines. With the help of a neighborhood friend and college student, he sneaked into the viewing gallery in the operating theaters at Columbia University's College of Physicians and Surgeons. To practice surgery, he performed operations in his basement on rabbits, rats, and stray cats, not losing a single patient. Starting at age 16, he volunteered for summer jobs at local hospitals near his family's vacation home in Port Washington on Long Island.

After leaving home in the fall of 1933, Koop enrolled at Dartmouth College on a football scholarship, majoring in zoology. There he met the woman who became his wife of over 60 years, Betty Flanagan. While at Dartmouth, he decided to give up football after sustaining an eye injury and receiving a warning from the school ophthalmologist that he was endangering his future as a surgeon. After graduating and receiving a bachelor of science degree at Dartmouth in 1937, Koop returned to New York City to enroll at Cornell University Medical College, a campus of Cornell on the Upper East Side of Manhattan. A year later he married Betty, a doctor's daughter and a hospital secretary. They had four children: Allen, born in 1944; Norman in 1946; David in 1947; and Betsy in 1951.

After receiving his MD from Cornell, Koop arrived in Philadelphia, Pennsylvania, in the summer of 1941 and took up a year-long internship at Pennsylvania Hospital. He then went on to pursue his postgraduate training at the University of Pennsylvania School of Medicine, the Boston Children's Hospital, and the Graduate School of Medicine at the University of Pennsylvania, where he received his doctor of science (medicine) degree in 1947. In 1946, Koop left Boston and returned to Philadelphia to establish the first pediatric surgical division at the Children's Hospital of Philadelphia. Koop succeeded despite initial resistance from some pediatricians and general surgeons who did not agree that the hospital needed a specialist in pediatric surgery.

Already a respected pediatric surgeon, Koop was named surgeon-in-chief of the Children's Hospital of Philadelphia in 1948. At this time, pediatric surgery was not yet a recognized medical specialty and posed a great challenge to the skilled 29-year-old surgeon. Nevertheless, he became a pioneer in the field of pediatric surgery, establishing the nation's first neonatal surgical intensive care unit in 1956. While a surgeon in Philadelphia, Koop performed ground-breaking surgical procedures on conjoined twins. After several promotions, he was named professor of pediatric surgery at the University of Pennsylvania School of Medicine in 1959.

After serving as surgeon-in-chief for 35 years, Koop left the hospital in 1981. He became internationally known for his speeches, publications and films, and rose to prominence among anti-abortion activists. This attracted the attention of newly-elected president Ronald Reagan, who appointed Koop as deputy assistant secretary for health in February 1981, with the promise that he would be nominated as surgeon general. Eight months of controversy and congressional hearings followed his nomination, with critics and supporters debating his stance on abortion and on whether or not he was qualified to address the health needs of the nation as a whole after devoting his career to treating individual patients. Many were also concerned that he would use the position of surgeon general as a platform for his anti-abortion views, delaying the confirmation process. But he was finally appointed and confirmed by the Senate on November 16, 1981, and at age 65, he was officially sworn in as surgeon general on January 21, 1982. The National Institutes of Health, the National Center for Disease Control, the Public Health Service (PHS), and the National Institute of Drug and Alcohol Abuse were under his command.

With a staff of only five and a budget of $500,000, Koop used his obscure office in the Washington suburb of Rockville, Maryland, to become the health conscience of a nation. One of his first official acts as surgeon general was appointing the position of deputy surgeon general to Faye Abdellah, the first woman to hold the post and the highest-ranking uniformed woman in the United States. Before Koop came on board, Abdellah had served the PHS for 25 years. Koop helped her establish Abdellah's laws, which set standards for patient comfort and forced the government to establish criteria for long-term care in nursing homes. Koop and Abdellah shared similar interests, including the care of handicapped children and their families, the expansion of self-help and mutual aid groups, innovative opportunities for the elderly, long-term nursing care, and continuing nursing education. Koop had Abdellah by his side during his eight years as surgeon general.

In February 1982, Koop received a letter from Luther L. Terry, the former surgeon general who released the first report on the health hazards of smoking in 1964. Koop had been on the same faculty with Terry at the University of Pennsylvania before Terry went to Washington. Koop had known Terry when he served as surgeon general and then also in his post-government service. With Terry's advice, Koop did what he could to preserve the integrity of the PHS, which had been suffering from low morale after the closing of PHS hospitals and the cut-back in personnel in the early 1980s. During his two terms as surgeon general, Koop became the most prominent government spokesman and advised the American public on a variety of health issues, including smoking and health, diet and nutrition, environmental health hazards, and the importance of immunization and disease prevention.

Over the course of his eight years as surgeon general, Koop devoted his time to the dangers of smoking more than any other issue. In 1981, the year Koop became the U.S. surgeon general, smoking had taken the lives of nearly 400,000 Americans, more than all deaths from alcohol, drug abuse, and automobile accidents combined. Koop gave continuous warnings on the health risks of smoking and helped reduce the number of smokers among Americans from 33 percent of the population in 1981 to 26 percent in 1989. However, the incident of illness and death increased among women during this period.

In 1982, Koop testified before Congress in favor of a series of rotating labels warning against the specific dangers (heart disease, cancer, emphysema, the risk to unborn children of pregnant women who smoke) in place of the current single generic label: "Warning: The Surgeon General Has Determined That Cigarette Smoking Is Dangerous to Your Health." Koop succeeded in 1986, having the surgeon general's health warning placed on packages of smokeless tobacco (chewing and snuff tobacco), a product that the tobacco industry suggested was a less harmful alternative to cigarettes.

In 1984, the twentieth anniversary of former U.S. Surgeon General Terry's Report on Smoking and Health from 1964, Koop launched a drive to enlist Americans in the fight against smoking, laying out the goal of his Campaign for a Smoke-Free Society by 2000. This effort not only warned of the dangers of smoking, but also urged smokers to quit in the presence of other people, emphasizing the health effects of second-hand smoke and the rights of nonsmokers as well. Koop became the first public health official to recognize the health consequences of bystanders and helped to create the most successful anti-smoking movement in the world. This has led to legal bans on smoking in federal buildings, as well as in public buildings such as offices, restaurants, and numerous other work sites in a growing number of states.

Perhaps most important of all, Koop helped the nation face what became the most fearsome new pandemic of the century: AIDS. He was instrumental on educating the public on prevention and protection, arguing against mandatory testing and quarantine of the infected and denouncing discrimination against AIDS sufferers in schools, the workplace, and housing. Koop gave the public reassurance that the AIDS virus could be spread by casual contact. On October 22, 1986, Koop issued his report on AIDS, stating that "there is now no doubt that we need sex education in schools and that it must include information on heterosexual and homosexual relationships." Koop's report did not come without its detractors and doubters, which included Fundamentalist and Roman Catholic leaders, antiabortionists, opponents of the gay lobby, and psychologists worrying about the impact of AIDS messages to the young. Critics feared that the mention of abortion in classes would make it seem like an easy solution to an offhand mistake. "The way sex education is taught in the schools encourages experimentation," said conservative social activist Phyllis Schlafly. "It's the cause of promiscuity and destroys the natural modesty of girls." But Koop threw the naysayers on the defensive and overcame his critics, changing the nature of sex education as we know it today.

One of the most controversial subjects that surrounded Koop during his tenure was the abortion issue. As an evangelical Christian, Koop had strongly opposed abortion throughout his life, but was criticized for betraying his anti-abortion principles after making a statement regarding pregnant women with AIDS, following his speech on AIDS in March 1987. When asked if a pregnant woman with AIDS should be counseled about abortion, Koop responded saying that he would not personally recommend an abortion, but that the woman should receive advice on abortion because of the risk of transmitting the disease to her unborn child. Abortion proved to be the most pressing issue of Koop's tenure because it blurred the lines between public health and personal moral choices. He was disturbed by the criticism he received that he had abandoned his stance on abortion. "How could I ever accept the destruction of the unborn after a career devoted to the repair of imperfect newborns, knowing the joy and fulfillment they brought to their families?" he said. After the U.S. Supreme Court's decision in Roe v. Wade legalized abortion in 1973, Koop made his feelings on the subject known in a book, The Right to Live, The Right to Die in 1976, and in 1979, he and theologian Francis Schaeffer produced Whatever Happened to the Human Race?, a multimedia project of five films and complementary lectures and seminars.

After serving as surgeon general for nearly eight years, Koop resigned from the post on October 1, 1989, one month before the official end of his second term. He was replaced by James O. Mason, who became acting surgeon general under then President George H.W. Bush. Koop then focused his attention on other efforts, becoming the chairman of the National Safe Kids Campaign and helping to reduce accidents among children. Throughout the 1990s, Koop continued to be a force for health care reform through his writings, public appearances, and personal contacts. He also promoted the use of the Internet for disseminating health information. In 1991, he had his first autobiography published, Koop: The Memoirs of America's Family Doctor, in which he wrote about the death of his son David from a rock climbing accident in 1968. He and his wife also dealt with this loss in a jointly-written book, Sometimes Mountains Move. In September 1995, President Clinton presented Koop with the Presidential Medal of Freedom, the nation's highest civilian award. He has been the recipient of other numerous honors and awards and is a prominent member of numerous professional societies and organizations.

In February 2007, his wife of 68 years, Elizabeth, died. They have three surviving children, seven grandchildren, and six great grandchildren. Koop is currently senior scholar at the C. Everett Koop Institute at Dartmouth College, an educational and outreach facility devoted to health promotion and preventive medicine. He is also the Elizabeth DeCamp McInerny professor of surgery at Dartmouth Medical School. He remarried on April 17, 2010, to Cora Hogue of Philadelphia, and they currently live in Hanover, New Hampshire.