In 2003, she received the Benjamin Franklin Medal for Distinguished Achievement in the Sciences of the American Philosophical Society. In 2009, Dr. Rowley was awarded the Presidential Medal of Freedom, the United States' highest civilian honor, by then-President Barack Obama, and the Gruber Prize in Genetics. Then in 2010, she was awarded the Jesse Stevenson Kovalenko Medal by the National Academy of Sciences. In 2012, Dr. Rowley was selected for the Hope Funds for Cancer Research Award of excellence in the area of Basic Research and was elected to the Hope Funds Scientific Advisory Board. Also in 2012, she won the Japan Prize for Healthcare and Medical Technology with two other scientists for her role in the creation of Gleevec. For Rowley's scientific contributions she has received honorary doctor of science degrees from multiple institutions some of which include Yale University and Harvard University. She is also a member of multiple scientific and honorary societies. These distinguished groups include the American Academy of Arts & Sciences and the National Academy of Sciences. She published more than five hundred articles and continued her research at the University of Chicago until shortly before her death. In 2017, she was posthumously inducted into the National Women's Hall of Fame.