A group of more than 70 volunteers from nearby Somerset churches will man the church tent so it's open 24 hours a day.
Almost 177,000 people are expect to camp at the music spectacular and the Church hopes some of them may be tempted to spend time praying.
Glastonbury runs until Sunday and acts include Florence and the Machine, Motorhead, Mark Ronson and Scottish pop star LuLu.
Revd Chris North a in the Diocese of Bath and Wells, is leading the volunteers.
He said the tent, located opposite the main Pyramid Stage, would provide a warm welcome and shelter.
There's space for 120 campers to sleep, if they are unable to find their tent.
Revd North said: "Over a year of planning goes into organising the Church Tent, so it's great to get on site and get set up.
"We're here round the clock during the festival, offering welcome, welfare and shelter to anyone who needs it."
Christine the rector of Pilton with the Chaplains to #Glasto out to see the sights pic.twitter.com/ZXVUEMNHQB
— OurChurchofEngland (@OurCofE) June 25, 2015