Eldo Kim, 20, faces up to five years in prison, three years supervised release and a USD 250,000 fine if convicted under a bomb hoax statute in connection with Monday's scare on campus.
He allegedly wasted the time of dozens of FBI, police and emergency workers after sending identical emails to Harvard University police, college officials and the student newspaper.
The email received Monday at 8:30 am, half an hour before Kim's exam was to start, was entitled "bombs placed around campus" and warned shrapnel bombs had been put in four buildings.
The message added "be quick for they will go off soon."
Police called in the FBI and the four buildings were swiftly evacuated, forcing the cancellation of a series of exams, but after hours of searching no explosive devices were found.
The emails were sent anonymously but an FBI affidavit said Kim confessed to officers that he did it to avoid a final exam scheduled that morning.
Kim will appear before a Massachusetts district court in Boston today, said US attorney Carmen Ortiz.
Harvard said in a statement that it was aware one of its students had been arrested in connection with the hoax.
"Yesterday was a day of significant disruption to our campus and a difficult time for many in our community," it said.
"We are aware that a Harvard student has been arrested in relation to this matter, and would be saddened if these allegations are substantiated and a member of our community had been involved in causing yesterday's disruption."
The university said it would not comment further on an ongoing criminal investigation.
The Ivy League school is one of the most prestigious universities in the world. It has about 21,000 students and dominates the Massachusetts town of Cambridge, near Boston.
Last month Harvard's great rival Yale went on a four-hour lockdown after a hoax caller claimed his roommate was planning to shoot people on campus.