Since you do not specify which movie you mean, I will assume you mean the most recent one (2003) by P.J.Hogan.
Peter Pan was originally a theatre play which opened in London in 1904. In 1911, the play was turned into a novel called, "Peter Pan and Wendy".
Aside from the differences in narrative form between a play and novel, the book contained an additional part where Peter Pan comes back to the Darling's house 20 years later only to find that Wendy has grown up and has a daughter. Peter then befriends the daughter Jane, and Jane promises to go to Neverland with Peter and be his 'mother' therefore replacing Wendy. This is one significant difference.
The 2003 film version was panned by audiences and critics for its 'action' type style and one notable difference was that the film chose to play up a romantic side to Peter and Wendy's relationship which in the book is described in vague terms. The film was criticized for being too explicit about their relationship and many people were angry at the suggestion that there was anything romantic about the relationship. After all Peter in his innocence wants Wendy to be his mother at times in the book.
Wikipedia has a lengthy article describing all the film versions of the play and the novel.