On July 14, 2004, barely two months after President Bush was forced to end National Security Agency domestic internet metadata collection by Attorney General John Ashcroft, Kollar-Kotelly issued a Foreign Intelligence Surveillance Act (FISA) court order allowing the NSA to resume domestic internet metadata collection.

In August 2007, she ordered the administration of George W. Bush to give its views regarding records requests by the American Civil Liberties Union on the National Security Agency's wiretapping program.

[8] On October 1, 2007, Kollar-Kotelly reversed George W. Bush on archive secrecy in a 38-page ruling, which said that the U.S. Archivist's reliance on the executive order to delay release of the papers of former presidents is "arbitrary, capricious, an abuse of discretion and not in accordance with law.

"[9] The National Security Archive at George Washington University alleged that the Bush order severely slowed or prevented the release of historic presidential papers.

The change of rule which she blocked had been enacted by the United States Department of the Interior after being supported by 51 members of Congress and passing an extended public comments period.

[13] Kollar-Kotelly presided over the Espionage Act case against Dr. Stephen Jin-Woo Kim after he told a reporter that North Korea would test its nuclear program.

[16] On May 14, 2024, Kollar-Kotelly sentenced Lauren Handy to 57 months in prison and three years of supervised release for her part in blocking access to an abortion clinic, a violation of the FACE Act.

During sentencing, Kollar-Kotelly addressed concerns raised by Harlow’s husband, John, and her attorney, who pleaded for leniency due to her rapidly declining health, warning that imprisonment could endanger her life.