The alleged acts happened in the mid 1990s at St. John the Baptist Catholic School in Costa Mesa, where Lyons served as a priest.
"Our community has waited a long time for justice in the case of this defendant," said Tony Rackauckas, Orange County District Attorney.
In 2003 authorities charged Lyons with lewd acts upon a child, involving three boys between 1978 and 1981. The case was dismissed after the U.S. Supreme Court ruled it was unconstitutional to file sexual charges that go back infinitely. So the statute of limitations had expired in that case.
With the latest charges, the alleged victim, who is now 24 years old, came forward last year. In a statement the Diocese of Orange says Lyons was removed from the ministry in 2002.
"The Diocese of Orange has cooperated fully with law enforcement during their investigation and will continue to do so. We remain committed to ensuring the events of the past are never repeated and encourage all to pray for the victims of sexual abuse and their families," wrote Ryan Lilyengren, Spokesperson, in a statement from the Diocese of Orange.
The Diocese of Orange has paid more than $4 million in settlements related to sex abuse claims involving Lyons. Investigators are concerned there may be other potential victims.
"For the past few years, Denis Lyons has lived in Leisure World, where many grandchildren and residents visit," said Rackauckas.
Lyons remains in custody, held on $100,000 dollars bail. If convicted of all the charges, Lyons could face up to 14 years in prison.