Lyons is accused of masturbating the boy between the years 1992 and 1995, when the child was 7 to 9 years old. The acts are alleged to have taken place in the church rectory, or Lyons' private quarters and office and in the sacristy, the church's storage room for religious garments, documents and vessels.
The Orange County Dist. Atty.'s Office has been trying to prosecute Lyons for years.
Prosecutors initially filed charges against Lyons in 2003 for allegedly molesting three boys at the same Coast Mesa church in the late 1970s and early '80s.
The charges had to be dropped after the U.S. Supreme Court put a statute of limitations on prosecuting molestation cases.
Because the alleged crimes took place before 1988, the year the court set as the earliest that crimes could be prosecuted in California, charges against Lyons were thrown out.
The Roman Catholic Diocese of Orange County last year settled a civil suit against Lyons and the church with Lyons' alleged victim.