The US announced charges against Abu Agila Masud two years ago, alleging he had played a key role in the bombing on 21 December, 1988.
The blast on board the Boeing 747 left 270 people dead.
It is the deadliest terrorist incident to have taken place on British soil.
All 259 passengers and crew on board the jumbo jet bound to New York from London died while another 11 people were killed in Lockerbie when wreckage destroyed their homes.
Last month it was reported that Mr Masud had been kidnapped by a militia group in Libya, leading to speculation that he was going to be handed over to the American authorities to stand trial.
A US Justice Department spokesperson told the Reuters news agency that the suspect would make an initial appearance in a federal court in Washington.
Five years ago he was serving a prison sentence in Libya for bomb-making.
In 2001 Abdelbaset al-Megrahi was convicted of bombing Pan Am 103 after standing trial at a specially convened Scottish court in the Netherlands.
He was the only man to be convicted over the attack.
Megrahi was jailed for life but was released on compassionate grounds by the Scottish government in 2009 after being diagnosed with cancer.
He died in Libya in 2012.
It is alleged that while in jail in Libya, Mr Masud confessed to being involved in the conspiracy with Megrahi to blow up the flight.
Aamer Anwar, Megrahi’s lawyer, said Mr Masud was actually in the custody of a warlord “widely condemned for human rights abuses” – he said the circumstances in which such a confession was extracted would be “strongly opposed” in any US or Scottish court.
Megrahi, who always proclaimed his innocence, launched two appeals against his 27-year sentence. One was unsuccessful and the other was abandoned.