The case is believed to be the first involving physical abuse, rather than sexual molestation, DutchNews.nl reported. A court is to hear the case March 11.
The man, now 59, has already received 25,000 euros ($32,750) in damages for sexual abuse he suffered at the boarding school in Limburg.
The man told the newspaper Volkskrant that the church has taken steps to address sexual molestation but not the kind of physical abuse he suffered.
"I was literally beaten into hospital five times," he said. "But the church does not comment on this sort of abuse."
His lawyer, Martin de Witte, said the church keeps a registry of sex offenders but not of priests or others who beat children.
'This is another example of the formal way some church authorities deal with victims," de Witte told Volkskrant. "They only do what is strictly necessary."