From 1998-2009 Dr. Klausner was a Deputy Health Officer, Director of STD Prevention and Control Services at the San Francisco Department of Public Health, member of the UCSF School of Medicine faculty in the Divisions of AIDS and Infectious Diseases and Attending Physician at San Francisco General Hospital. While in San Francisco Dr. Klausner helped identify key factors associated with the increased spread of HIV and STDs and implemented multiple novel public health prevention programs. He helped create the St. James Infirmary, the first occupational health and safety clinic for sex workers and Magnet, a community-based peer-run sexual health clinic for gay men. From 2009-2011 Dr. Klausner was Branch Chief for HIV and TB at the Centers for Disease Control in Pretoria, South Africa, helping lead the South African PEPFAR program for care and treatment.

After returning from South Africa, from 2011-2021 Dr. Klausner was a senior faculty member in the UCLA Division of Infectious Diseases, David Geffen School of Medicine and the Department of Epidemiology at the Fielding School of Public health. At UCLA, Dr. Klausner was the Principal Investigator for multiple NIH-funded networks, projects and studies on sexually transmitted infections and antimicrobial resistance in Peru, Botswana, South Africa, Vietnam, Haiti, Pakistan and India.

Currently, Dr. Klausner is a Professor of Population and Public Health Research and Professor of Medicine, Division of Infectious Diseases, at the Keck School of Medicine of the University of Southern California.

Dr. Klausner's research interests are in applied epidemiology and the prevention and control of infectious diseases of public health importance like HIV, STDs, TB, COVID-19 and cryptococcal infections. Dr. Klausner has a particular interest in the use of technology — information, digital, and laboratory — to facilitate access to treatment for disadvantaged populations. Dr. Klausner has been funded by the NIH, CDC, private pharmaceutical and test manufacturers to study the benefits of new ways to find and treat infectious diseases. Dr. Klausner is a frequent advisor to the CDC, NIH and WHO and a popular public speaker.