“Regina has served as America's doctor since 2009 and has impacted the health and lives of Americans across the country. I am deeply grateful for her leadership and service,” she wrote.
Benjamin said she intended to remain involved in public health issues.
The surgeon general pushed efforts to combat obesity and smoking during her tenure.
Last year Benjamin released a report warning that tobacco use among young adults was growing, despite years of anti-smoking campaigns and calls for more government action. She also launched the “Every Body Walk” campaign to promote physical activity.
The American Public Health Association called Benjamin a “remarkable advocate in promoting the value of prevention.”
"We are extraordinarily grateful for her strong public health leadership," the group said in a statement.
Before being tapped for surgeon general in 2009, Benjamin worked at the Bayou La Batre Rural Health Clinic, which she founded to serve gulf coast residents in Alabama.
This story was updated at 8:58 a.m.