The Burlington County Prosecutor's office says Joseph V. Pullen Jr., of Pemberton Township assaulted the child during a July 8 service at Calvary Baptist Church.
Authorities say Pullen, a church deacon, was alone with the victim at the time, although a service was under way.
It is not clear immediately clear if he has a lawyer. A message left for church officials was not returned.
Pullen was arrested Friday and is being held on $250,000 bail.
Prosecutors say an investigation into the incident revealed that Pullen had allegedly assaulted the same victim in 2011 at a different location.
Pullen faces charges in both incidents, including sexual assault, sexual contact and child endangerment.