Fowler's scientific excellence and achievements have been recognized by prestigious awards, including the National Medal of Science, awarded in 2009 by President Obama. In 2003, Fowler was elected to the National Academy of Sciences.
Her numerous other honors include: 
* 1997 – Society of Nuclear Medicine's Paul C. Aebersold Award for outstanding achievement in basic science
* 1998 – American Chemical Society's Francis P. Garvan-John M. Olin Medal
* 1998 – E.O. Lawrence Award, awarded by the Department of Energy
* 2000 – Society of Nuclear Imaging in Drug Development's Alfred P. Wolf Award
* 2002 – American Chemical Society's Glen T. Seaborg Award for Nuclear Chemistry
* 2005 – Distinguished Basic Scientist of the Year Award from the Academy of Molecular Imaging (AMI)
* 2008 – National Medal of Science, administered by the National Science Foundation and bestowed by the president of the United States
* 2009 – National Academy of Science Award in Chemical Sciences, awarded by the National Academy of Sciences
* 2011 – Distinguished Women in Chemistry/Chemical Engineering Award, sponsored by the American Chemical Society
* Distinguished Scientist Fellowship, sponsored by the Department of Energy's Office of Biological and Environmental Research