Custer County ranked 45th among 57 South Dakota counties scored on the basis of health outcome in 2013, which is down from 2012 primarily because the number of premature deaths per  100,000 increased by over 1,500, raising the number above the national average. The county ranked 11th when health factors were reviewed. Data does not indicate health behaviors deviate significantly from state averages, though the percentage of the adults who smoke or drink excessively exceeds national averages, and the incidence of sexually transmitted infections is also high when compared to state and national statistics. Clinical care indicators note that 14 percent of the population is uninsured. Approximately one in five children live in poverty and one in four live in single-parent homes. This information was compiled by the Population Health Institute at the University of Wisconsin in conjunction with the Robert Wood Johnson Foundation. To compare Custer County to other counties, go to: County Health Rankings: Mobilizing Action Toward Community Health.

The Custer County Office of Community Health Services and Public Health Alliance provides public health services to all ages. The office manages various primary and preventive programs that help residents develop and maintain a healthier lifestyle and higher quality of life. Professional nursing and nutrition staff provide advice to individuals, families and communities. The office also provides a wide range of services to infants, children, pregnant and postpartum women and adults.