Frieden has served as commissioner for the past seven years, where he led a campaign to ban smoking in restaurants and bars, boosted the number of New Yorkers getting HIV tests and helped to distribute millions of free condoms.
In a statement announcing Frieden's appointment, Mr. Obama said the new CDC chief had been a "leader in the fight for health care reform, and his experiences confronting public health challenges in our country and abroad will be essential in this new role."
Frieden will inherit a looming decision on how best to manage a swine flu outbreak, including whether or how to produce a swine flu vaccine. The virus has infected 6,673 people in 35 countries.
The White House said Frieden will begin at the CDC in early June.
Health experts say the CDC needs to make immediate improvements in employee morale and organization as the Obama administration works to overhaul the national health care system.
"Dr. Frieden is an expert in preparedness and response to health emergencies, and has been at the forefront of the fight against heart disease, cancer and obesity, infectious diseases such as tuberculosis and AIDS, and in the establishment of electronic health records," Obama said in the statement.
Frieden, 48, is expected to take office next month. His appointment does not require Senate confirmation.
He will succeed Dr. Julie Gerberding, who resigned in January. Dr. Richard Besser has served as acting head of the Atlanta-based CDC in recent months.
The White House announcement said Besser, who has led the CDC's Coordinating Office for Terrorism Preparedness and Emergency Response for the past four years, would return to that position.