After completing her PhD, Kieny took up a position at Transgene SA, Strasbourg, as assistant scientific director under scientific director Jean-Pierre Lecocq until 1988. Kieny became director of research at Insermfor the first time between 1999 and 2000. Kieny was a member of the European Vaccine Initiative until 2010. Kieny was vaccine research director of WHO from 2002-2010, most notably during the 2009 swine flu pandemic. She was promoted to assistant director-general, playing a major leadership role during the Ebola virus epidemic in West Africa and the 2015–16 Zika virus epidemic. Kieny even audaciously signed up herself as a test subject for the safety of new Ebola vaccines being developed, amidst concerns over the logistics and ethics of testing early-stage therapeutics and preventatives for ebola in the context of an ongoing epidemic. Given the slow development of new therapies in response to the outbreak, Kieny and colleagues began making a framework to speed up development and encourage researchers to share data openly without worrying about being scooped. She commented on the successful development of efficacious vaccines for deployment in a future outbreak. In aftermath of the 2014 Democratic Republic of the Congo Ebola virus outbreak Kieny stated that the vaccine may not be required since the outbreak was not as serious as previously feared. Kieny was involved also in addressing the ongoing antimicrobial resistance crisis with WHO, overseeing the first WHO Model List of Essential Medicines to include guidance on proper use of antibiotics within the framework of universal health care. She helped prepare a list of Antibiotic resistant bacteria which should be prioritised for research beyond just Extensively drug-resistant tuberculosis, such as Acinetobacter baumannii and Pseudomonas aeruginosa strains resistant to Carbapenem. Kieny was one of seven vaccine experts interviewed in 2012 by Wired about what the next decade held for vaccine innovation. In 2017 she joined the board of directors for the Human Vaccines Project, was made interim director of the Medicines Patent Pool, and joined the Drugs for Neglected Diseases Initiative as chief of the board. She also holds a position as an independent director of BioMérieux, and as an advisor for the GISAID. As head of MPP, Kieny oversaw the licensing of the Hepatitis C drug Mavyret for generic production.
