The film has many significant changes from the source novel. While elements of his journey around Europe as well as his amnesia are retained, the Jason Bourne of the novel is not an assassin but rather a deep cover CIA operative acting as a fictional assassin to get close to international assassin Carlos the Jackal; he was wounded attempting to prevent rather than perpetrate an assassination. The nature of Operation Treadstone is also different than portrayed in the film: Instead of a network of government sponsored assassins it is a scheme to trap Carlos with Jason Bourne as the sole field agent.

While most of the characters in the film share names similar with characters in the novel, their personalities and place in the story are significantly different. The character of Marie in the novel is a Canadian economist as opposed to a young, unemployed German traveller. Conklin is a more villainous presence in the film adaptation who, unlike in the novel, does not survive. The story thread involving Carlos was also removed as the real Carlos was by this time imprisoned in France. Bourne discovering information regarding his true identity and past — such as his real name — was also removed.