The Ivy League school said on its online alert system that all four buildings - three classroom facilities and a dorm - had reopened following a sweep by local, state and federal law enforcement officials.
"I am relieved to report that no suspicious devices were found," wrote Katie Lapp, a university executive vice president, in a message to the Harvard community. "At this time, we know of no specific threat to campus and activities are returning to normal."
The evacuations resulted in the cancellation of final exams for some classes at the Cambridge, Massachusetts, campus.
Institutions across the Boston area have been on an elevated state of alert since the April 15 bombing attack at the Boston Marathon that killed three people and injured 264.
The Harvard campus police, Cambridge Police and Massachusetts State Police, including the bomb squad, responded to the campus, where they set up yellow-taped perimeters around the evacuated buildings and directed students to move away.
During the search, university officials had closed Harvard Yard - the wooded and currently snow-covered historic center of the campus - to outside pedestrians, allowing only people who held Harvard identification to enter.
The school, founded in 1636, has about 21,000 students.
Daniel Banks, an 18-year-old freshman from Marlboro, New Jersey, was about to take a final exam in a government class when he was evacuated from Emerson Hall.
"It was my first final ever at Harvard and within a minute it was canceled," Banks said. "I never expected anything like this to ever happen at Harvard especially, but I'm glad that nothing real has happened yet."
It was the latest in a series of security scares at U.S. schools and universities. Three days ago a Colorado high school student intent on confronting a teacher opened fire at his school, severely wounding a classmate before killing himself.
Late last month Yale University in New Haven, Connecticut, placed its campus on lockdown for most of a day after an anonymous caller warned officials that his roommate was headed to the school planning to shoot people. No gunman was found and police now regard the incident as a hoax.
"I've been here eight years and we've had a couple of one-off incidents, but nothing of this scale," said Travis Lovett, 33, of Wakefield, Massachusetts, who works at Harvard.