Warning: The following is full of spoilers
*The novel is in chronological order, while the film is not.
*In the novel, when Alex comes back from going to the mall after killing the security guard, there is a moment where Alex calls Jared and Jared is talking about his trip to Oregon State, and why Alex took his clothes (in the novel, it's mentioned that he took Jared's clothes and threw his away.)
*In the novel, the security guard's death is a lot more graphic. In the film he just hits the security guard who falls backwards onto a different set of tracks. In the novel, Alex and Scratch jump off the train, and Scratch is briefly assaulted by the security guard, before Alex hits him with his board. The security guard then falls next to the train tracks, and is dragged by the train, before folding underneath it, and then getting cut in half by another car.
*After he kills the security guard, in the novel, Alex briefly examines the car.
*In the novel, the part where Alex is walking back to Jared includes him bumping into some strangers
*In the movie, the security guard attacks Scratch and Alex with a flashlight. In the novel, it's a nightstick.
*The movie cuts out the entire end in the novel, where Alex returns to Paranoid Park, and gets assaulted by Scratch's friends.
*Alex's friends (besides Jared) are downplayed in the movie, then they are in the novel.
*In the movie, it's implied that Alex's girlfriend is upset because she thinks he was dating her just to have sex. In the novel, it's explicitly stated