Frieden has served as New York City's health commissioner for the past seven years. In that time, he spearheaded 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.
Frieden also worked for the CDC from 1990 to 2002 in part as a CDC Epidemiologic Intelligence Service Officer, where he investigated the spread of multidrug-resistant tuberculosis.
In a statement, the president acknowledged Frieden's work in emergency preparedness.
"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. Dr. Frieden has 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," Obama said.
Frieden takes the place of Richard Besser, who was the acting director and managed the CDC response to the H1N1 outbreak. As part of his job, Frieden will determine whether or how to produce a swine flu vaccine. On Friday, the government announced the fourth person in the U.S. who died of the flu.
Besser will retain his post as head of the CDC's Coordinating Office for Terrorism Preparedness and Emergency Response.
"Secretary Sebelius and I thank Acting CDC Director Dr. Rich Besser and the women and men throughout the CDC for their superb work, especially over the past weeks," Obama said, referring to his health and human services chief, Kathleen Sebelius. He said Besser's "preparations were essential during the recent H1N1 flu detection and response activities. We are very pleased he will continue in that role."
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.
"I think the administration selected Tom Frieden because he can take public health to a new place," Jeffrey Levi, executive director of Trust for America's Health, a nonprofit public health advocacy organization, told The New York Times. "He's a transformational leader."
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.
The Associated Press contributed to this report.