Satcher served simultaneously in the positions of Surgeon General and Assistant Secretary for Health from February 1998 through January 2001 at the US Department of Health and Human Services. As such, he is the first Surgeon General to be appointed as a four-star admiral in the PHSCC, to reflect his dual offices. In his first year as Surgeon General, Satcher released the 1998 Surgeon General's report, "Tobacco Use Among U.S. Racial/Ethnic Minority Groups." In it he reported that tobacco use was on the rise among youth in each of the country's major racial and ethnic groups threatening their long-term health prospects. Satcher was appointed by Bill Clinton, and remained Surgeon General until 2002, contemporaneously with the first half of the first term of President George W. Bush's administration. Eve Slater would later replace him as Assistant Secretary for Health in 2001. Because he no longer held his dual office, Satcher was reverted and downgraded to the grade of vice admiral in the regular corps for the remainder of his term as Surgeon General. In 2001, his office released the report, The Call to Action to Promote Sexual Health and Responsible Sexual Behavior. The report was hailed by the chairman of the American Academy of Family Physicians as an overdue paradigm shift—"The only way we're going to change approaches to sexual behavior and sexual activity is through school. In school, not only at the doctor's office." However, conservative political groups denounced the report as being too permissive towards homosexuality and condom distribution in schools. When Satcher left office, he retired with the rank of vice admiral.
Post–Surgeon General
Upon his departure from the post, Satcher became a fellow at the Kaiser Family Foundation. In the fall of 2002, he assumed the post of Director of the National Center for Primary Care at the Morehouse School of Medicine. On December 20, 2004, Satcher was named interim president at Morehouse School of Medicine until John E. Maupin, Jr., former president of Meharry Medical College assumed the current position on February 26, 2006. In June 2006, Satcher established the Satcher Health Leadership Institute at Morehouse School of Medicine as a natural extension of his experiences improving public health policy for all Americans and his commitment to eliminating health disparities for minorities, the poor, and other disadvantaged groups. In 2013, he co-founded the advocacy group African American Network Against Alzheimer's. He now sits on the boards of Johnson & Johnson and MetLife.
Criticisms of health inequality
While acknowledging progress, Satcher has criticized health disparities. He asked the question, “What if we had eliminated disparities in health in the last century?” and calculated that there would have been 83,500 fewer black deaths in the year 2000. That would have included 24,000 fewer black deaths from cardiovascular disease. If infant mortality had been equal across racial and ethnic groups in 2000, 4,700 fewer black infants would have died in their first year of life. Without disparities, there would have been 22,000 fewer black deaths from diabetes and almost 2,000 fewer black women would have died from breast cancer; 250,000 fewer blacks would have been infected with HIV/AIDS and 7,000 fewer blacks would have died from complications due to AIDS in 2000. As many as 2.5 million additional blacks, including 650,000 children, would have had health insurance in that year. He called on people to work for solutions at the individual, community, and policy level. Satcher supports a Medicare-for-all style single payer health plan, in which insurance companies would be eliminated and the government would pay health care costs directly to doctors, hospitals and other providers through the tax system. In 1990, while President of Meharry Medical College, Satcher founded a quarterly academic journal entitled the Journal of Health Care for the Poor and Underserved. Both the Kaiser Family Foundation and the Medical Library Association rate this journal as one of the nation's important public health journals.