Some funny but clean jokes about church are "The Holy Family" and "Adam's Ribs." In "The Holy Family," a Sunday Bible teacher asks her students why Joseph and Mary took Jesus with them to Jerusalem. A small child answers, "They couldn't get a babysitter."
In "Adam's Ribs," little Johnny's mom sees him lying down and asks him what's the matter. He says his ribs are painful, and he thinks he's having a wife in reference to the Bible story of how Eve was created from one of Adam's ribs. Another joke is about "Applying the 10 Commandments." A Sunday school teacher teaches her five and six year old students the commandment "Honor your father and mother." A kid asks whether there is a commandment on how to treat siblings, to which another kid quips, "Thou shalt not kill."
Jokes.ChristiansUnite.com has a joke called "The Army of the Lord." After church service, the pastor waits at the door to shake each churchgoer's hand as they leave. When it is the turn of a frequently absent member, the preacher grabs his hand and chides him, "You must join the Army of the Lord." The man replies, "But I already serve in the Army of the Lord." "Why do I never see you save for Christmas and Easter?" asks the pastor. The man answers, "That's because I'm in the secret service."