After college Evanina went to work for the General Services Administration, where he was a project manager in the new construction division. In 1996 he joined the Federal Bureau of Investigation where as a special agent he served in the violent crimes unit, the organized crime unit, and the Bank Robberies and Counterterrorism divisions. He also later served in the FBI's National Security Branch and Counterintelligence Division. He became a certified SWAT team member as well as a certified sniper. During this time he was involved with the investigation into the hijacking of United Airlines Flight 93 on 11 September 2001, the mail-distributed anthrax attacks also in 2001, and the Daniel Pearl kidnapping.