A former student of Liberty University has claimed he had a sexual encounter with the wife of Jerry Falwell Jr 12 years ago.

The allegations against Becki Falwell come just days after her husband resigned as President of Liberty University, one of the biggest Christian colleges in the world. 

The resignation followed revelations of her affair with a pool boy and a photo posted by Falwell Jr of him with his pants unzipped, revealing part of his underwear. 

The unnamed former student of Liberty U told Politico that Becki Falwell performed oral sex on him when he stayed over at the Falwell family home following band practice with her son in 2008.  He says he was 22 at the time. 

He alleges that Becki continued to pursue him with Facebook messages and offers of gifts after he had rejected further advances.

"She was the aggressor," he said of the relationship.

An unnamed friend told Politico that the student had confided in him about the encounter with Becki within a month of it allegedly occurring. 

In a statement, Jerry and Becki Falwell denied the allegations.

"It is unfortunate that the coverage of our departure has turned into a frenzy of false and fantastic claims about us," they said.

"These false and mean spirited lies have hurt us and our family greatly and we will respond fully with the truth at an appropriate time.

"At this time, however, we think it is best to move on and help the Liberty community focus on its very bright future."