Shortly after becoming a Special Agent with the FBI, Rowley was assigned to the Omaha, Nebraska and Jackson, Mississippi Divisions. Beginning in 1984, she spent six years working in the New York Office on investigations involving organized crime. She also served in the U.S. embassy in Paris and the consulate in Montreal. In 1990, she was assigned to the FBI‘s Minneapolis office, where she became the chief legal adviser.[citation needed]

After the September 11, 2001, attacks, Rowley wrote a paper for FBI Director Robert Mueller documenting how FBI HQ personnel in Washington, D.C., had mishandled and failed to take action on information provided by the Minneapolis, Minnesota Field Office regarding its investigation of suspected terrorist Zacarias Moussaoui. Moussaoui had been suspected of being involved in preparations for a suicide-hijacking similar to the December 1994 „Eiffel Tower“ hijacking of Air France 8969. Failures identified by Rowley may have left the U.S. vulnerable to the September 11, 2001, attacks. Rowley was one of many agents frustrated by the events that led up to the attacks,