Francisco currently serves as the Presidents Distinguished Professor of Earth and Environmental Science and Professor of Chemistry at the University of Pennsylvania. He served as the [http://newsroom.unl.edu/releases/2014/04/25/Joseph+S.+Francisco+to+lead+UNL%27s+College+of+Arts+and+Sciences Dean] of [http://cas.unl.edu/ College of Arts and Sciences], Elmer H. and Ruby M.Cordes Chair in chemistry at University of Nebraska in Lincoln until 2018. He was president of the National Organization for the Professional Advancement of Black Chemists and Chemical Engineers from 2006 to 2008. He was appointed a senior visiting fellow at the Institute of Advanced Studies at the University of Bologna, Italy; Professeur Invité at the Université de Paris-Est, France; a visiting professor at Uppsala Universitet,Sweden; and an Honorary International Chair Professor, National Taipei University of Technology, Taiwan. He served as president of the American Chemical Society in 2010. He was elected as the Fellow of the American Academy of Arts and Sciences, 2010 and was elected member of the U.S. National Academy of Sciences in 2013. He also received the honorary Doctor of Science degree, Tuskegee University., 2010. President Barack Obama appointed Joseph S. Francisco, PhD, to serve on the Presidents Committee on the National Medal of Science for the period 2010–2012, 2012–2014.
In 2021 he was elected to the American Philosophical Society.