The Krafts have donated hundreds of millions of dollars to philanthropic work including education, child- and women-related issues, healthcare, youth sports and American and Israeli causes. Among the many institutions the Krafts have supported are Columbia University, Harvard Business School, Brandeis University, The College of the Holy Cross, Boston College, Tufts University, Yeshiva University, the Belmont Hill School, and the Boys & Girls Clubs of Boston.

In 1989, Myra and Robert Kraft launched the Passport to Israel Fund, in collaboration with Center for Jewish Progress of Greater Boston (CJP), to help parents send their teenage children to Israel. One of their most distinctive projects is supporting American Football Israel, including Kraft Family Stadium in Jerusalem and the Kraft Family Israel Football League. In 1990, Kraft, his wife, and his father-in-law funded a joint professorship between Brandeis University and Holy Cross College, forming the Kraft-Hiatt endowed chairs in comparative religion – the first inter-religious endowed chairs in the United States.

In 2011, the Krafts pledged $20 million to Partners HealthCare to launch the Kraft Family National Center for Leadership and Training in Community Health, an initiative designed to improve access to quality healthcare at community health centers throughout New England. The Krafts supported the Dana–Farber Cancer Institute in Boston.