Applicants may be ineligible due to incomplete or false application information, certain violations of federal security regulations, or disqualifying criminal offenses and factors. Global Entry, NEXUS, and SENTRI allow some foreign citizens to apply.

Approval for TSA PreCheck is denied to applicants who are deemed a potential security threat based on a criminal background check and a security threat assessment. Specific permanent disqualifying offenses include espionage, sedition, treason, terrorism, and murder. Additionally, there are "interim" disqualifying offenses where an applicant may be ineligible if they were convicted within the last seven years or released from incarceration within the last five years; these include crimes like extortion, bribery, and certain drug-related felonies. Furthermore, individuals who have committed serious aviation security violations, such as assaulting a flight crew member or interfering with security operations, may be suspended or permanently banned from the program. Applicants may also be denied if they are under indictment or have an active warrant for a disqualifying felony.