Lauri Love, 28, from Stradishall, Suffolk, is accused of breaching the systems to steal "massive quantities" of confidential data resulting in millions of dollars of losses.
He was arrested by officers from the UK's National Crime Agency (NCA) under the Computer Misuse Act (CMA) on Friday and later charged by US authorities in New Jersey.
Mr Love was a student at the university two years ago and was a member of a group who occupied educational buildings for several months in a protest over fees.
He is charged with one count of accessing a US department or agency computer without authorisation and one count of conspiring to do the same.
If convicted, he faces a maximum penalty of five years in prison and a $250,000 (£155,000) fine, or twice the total gain or loss from the offence.
NCA spokesman Andy Archibald said: "This arrest is the culmination of close joint working by the NCA, Police Scotland and our international partners.
"Cyber-criminals should be aware that no matter where in the world you commit cyber crime, even from remote places, you can and will be identified and held accountable for your actions."
The hacking is alleged to have taken place over the past 12 months. Love and co-conspirators - believed to be in Australia and Sweden - allegedly created "back doors" into government networks, allowing them to return to get data.