Mayo Clinic Health System in Eau Claire is a physician-led, integrated health care system. Its board of directors is composed of seven elected physicians, five community members, three physician members from Mayo Clinic Rochester and one Mayo Clinic Health System administrator. The board of directors sets the mission and vision of the organization, sets policy and directs the management to implement policy. The board reports to Mayo Clinic Health System in the northwest Wisconsin region, which reports to the Mayo board of governors and, ultimately, the Mayo board of trustees.

The organization is led by Richard Helmers, M.D., regional vice president, Northwest Wisconsin Region, Mayo Clinic Health System, who works closely with the Robert Peck, M.D., chief medical officer. This group, along with the chair of the Practice Committee, Jose Ortiz Jr., M.D., chief of staff, and Michael Morrey, regional chair of Administration, Northwest Wisconsin Region, Mayo Clinic Health System, are the top leadership of the organization. Physician matters are dealt with by the Practice Committee and the chief medical officer. A team of vice presidents report to the senior management group. Departments are led by a team of the department physician chair, director and vice president.