If you are talking about paper work, they have the same meaning, but "fill out" is usually used when a full document is being completed - "Please fill out this paper work."
"Fill in" can be used for a portion of a document - "Please fill in this line." or "Fill in the blank."
Though "fill in" can have other meanings:
"They had to fill in the hole in the wall with Spackle."
"I need you to fill in for him. He is sick." (Substitute for)