In 2013, Armstrong was appointed chair of medicine and physician-in-chief at Massachusetts General Hospital (MGH), becoming the first woman to hold the position. The day she began her tenure at MGH, the Boston Marathon bombing occurred and she said it enabled her to "see MGH come together in an extraordinary way to respond to the need of the community." In the same year, she was also elected to the National Academy of Medicine. Although she had left UPenn, Armstrong received their Pioneer Award for her "achievements and rise to some of the highest health care posts in government and academic medicine."