This funny-sounding expression indicates that someone just told a joke or isn't being serious! Someone who says something "tongue-in-cheek" is usually kidding.
It's believed that this saying was created by an English humorist in the 1800s. Most people have difficulty saying anything with their tongue in their cheek. But some people actually do stick their tongue against the inside of their cheek after saying a joke to show that they're only kidding.