The ordeal lasted for two hours on Wednesday evening at Harvest Orange County Church in Irvine, California.
According to local TV news station KCAL9, a security guard saw the two men walk into the lobby of the church carrying rifles. He called police straight after.
Greg Laurie is the pastor of the megachurch. He said police arrived on the scene within minutes and apprehended the suspects after having to find where they were in the building.
The men were described as walking out of the building "peacefully". It turned out that the suspects actually had fake rifles.
In a post on Facebook, Laurie added that the church building was left with minor damage from the incident but no one was injured.
The motive for the break-in is unknown.
Church services at Harvest Orange County Church will continue as normal but the church is ramping up security measures.