Her 2011 book, Area 51: An Uncensored History of America's Top Secret Military Base, about Area 51, makes the claim that the Roswell UFO incident was a Soviet plot to induce War of the Worlds style hysteria.^[3] The New York Times called it "noteworthy for its author’s dogged devotion to her research".^[1] Richard Rhodes, writing in The Washington Post, was more critical of her Roswell claim and its reliance on a single source, writing "Jacobsen shows herself at a minimum extraordinarily gullible or journalistically incompetent."^[4]

Jacobsen's 2014 book, Operation Paperclip: The Secret Intelligence Program That Brought Nazi Scientists to America^[5] was called "perhaps the most comprehensive, up-to-date narrative available to the general public" in a review by Jay Watkins of the CIA's Center for the Study of Intelligence.^[6] Operation Paperclip was included in a list of the best books of 2014 by The Boston Globe.^[7] Leading space historian Michael J. Neufeld gave a negative review of the book: "I cannot endorse Operation Paperclip because: it is error-ridden, it produces no fundamentally new information, it is unbalanced, and its notes are poor."^[8]

The Pentagon's Brain: An Uncensored History of DARPA, America's Top Secret Military Research Agency,^[9] was chosen as finalist for the 2016 Pulitzer Prize in history.^[10] The Pulitzer committee described the book as "A brilliantly researched account of a small but powerful secret government agency whose military research profoundly affects world affairs." The Washington Post, The Boston Globe and the Amazon Editors chose Pentagon's Brain as one of the best non-fiction books of 2015.

Her next book was published in March 2017: Phenomena: The Secret History of the U.S. Government's Investigations into Extrasensory Perception and Psychokinesis.^[11]

In May 2019, she released Surprise, Kill, Vanish: The Secret History of CIA Paramilitary Armies, Operators, and Assassins. Apple audiobooks recorded SKV as one of the most popular audiobooks of 2019.^[12] J. R. Seeger, a retired CIA case officer who led the Agency's Team Alpha, the first Americans behind enemy lines after 9/11, reviewed the book, saying: "Jacobsen has a well-deserved reputation as a good writer and an excellent researcher,” but he criticized her attention to detail, and suggested that the book's focus was too general saying that "neither of the topics are discussed in anything resembling the detail required to understand the nuance of covert action".^[13]

Jacobsen's most recent book was published in March 2024: Nuclear War: A Scenario.^[14][15][16] It is being adapted into a screenplay, by or Denis Villeneuve ^[17].

Jacobsen co-wrote three episodes of Tom Clancy's Jack Ryan TV series for Amazon Studios. She was a consulting and writing producer on all of seasons one and two.^[18]

In 2017, Amblin Entertainment and Blumhouse TV^[19] bought the rights to her book Phenomena for a scripted TV series, with Jacobsen and X-Files writer/producer Glen Morgan co-writing the pilot script.

In 2004, Jacobsen wrote an article about an incident she witnessed with a group of thirteen foreign nationals on board a flight from Detroit to Los Angeles. Two air marshals came out of cover during flight. FBI and homeland security agents met the aircraft when it landed.^[20]

In May 2007, the Department of Homeland Security declassified a report about the flight. The men were identified as twelve Syrians, members of a musical group, and a Lebanese, their promoter; all were traveling illegally on expired visas. Eight of the men had "positive hits" for past criminal records and suspicious behavior.^[21] They were involved in an earlier incident on an aircraft which had them on the FBI watch list. However, the report noted that the musicians were not terrorists and law enforcement assessments at the time were appropriate.^[22][23]

• Terror in the Skies: Why 9/11 Could Happen Again. Spence Publishing Company, 2005, ISBN 1-890626-62-7.
• Area 51: An Uncensored History of America's Top Secret Military Base, Hachette Digital, Inc., 2011, ISBN 1-4091-4113-6.
• Operation Paperclip: The Secret Intelligence Program that Brought Nazi Scientists to America. Little, Brown. 11 February 2014. ISBN 978-0-316-22105-4.^[24]
• The Pentagon's Brain: An Uncensored History of DARPA, America's Top-Secret Military Research Agency. Little, Brown and Company. 2015. ISBN 978-0316371766. OCLC 900012161.
• Phenomena: The Secret History of the U.S. Government's Investigations into Extrasensory Perception and Psychokinesis. Little, Brown and Company. 2017. ISBN 978-0316349369.
• Surprise, Kill, Vanish: The Secret History of CIA Paramilitary Armies, Operators, and Assassins. Little, Brown and Company. 2019. ISBN 0316441430.
• First Platoon: A Story of Modern War in the Age of Identity Dominance. Dutton. 2021. ISBN 978-1524746667.
• Nuclear War: A Scenario. Penguin Publishing Group. 26 March 2024. ISBN 978-0-593-47609-3.

• Appearances on C-SPAN
• NPR interview
• NPR's Fresh Air, "Was it UFOs or the USSR?" May 17, 2011
• Jacobsen on ABC Nightline
• Tavis Smiley interview
• The Daily Show, Jon Stewart, May 17, 2011
• Annie Jacobsen at IMDb
• Joe Rogan Experience #1299 - Annie Jacobsen