After the dismissal of Master Nathaniel Eaton in 1639 for gross negligence and mismanagement, Harvard College remained closed until 1640, when Henry Dunster was appointed as the first president. Harvard has never shut down completely since then.
18th century outbreaks of disease
Starting in 1730 and recurring various times later in the 18th
century, Commencement was cancelled, students dismissed, vacations extended, and other policies changed due to smallpox outbreaks. The Tolman index has many references to these events. The first references start on this card
In 1774 the Harvard Corporation voted “that there be no public Commencement this Year” due to British occupation of Boston. Ceremonies were held again in 1779, but Commencement did not resume as an annual event until 1781.
1918 influenza epidemic
While it appears that the Medical School closed for a period during this epidemic, the University did not shut down, although large classes and certain other gatherings were suspended.
“… in February 1978, a severe snowstorm forced University officials to close Harvard for three days. It is the only known closure due to snow in the University’s memory, according to Rev. Peter J. Gomes, Plummer Professor of Christian Morals, who teaches Religion 1513, ‘History of Harvard and its Presidents’.
“Even this closure occurred only after the Massachusetts governor declared a state of emergency, brought in the national guard, and restricted any unnecessary travel. After the blizzard hit, many people asked then University President Derek C. Bok why he did not immediately shut the University down. According to Gomes, Bok responded, ‘I tried to, but I didn’t know how.’”
Students remained on campus during the emergency.
Kent State Era, May 4, 1970 and beyond
Despite extensive disruption, the effective ending of the academic year in early May, 1970
, and public calls to close the University, Harvard did not formally shut down. Commencement took place on June 11, 1970.
 In the spring semester of 1970, final exams were scheduled to end on June 2.