"The court concludes international travel is not a mere convenience or luxury in this modern world. Indeed, for many international travel is a necessary aspect of liberties sacred to members of a free society," Brown wrote in her 65-page ruling.
"Accordingly, on this record the court concludes plaintiffs inclusion on the no-fly list constitutes a significant deprivation of their liberty interests in international travel," Brown said.
The 13 plaintiffs - four of them veterans of the U.S. military - deny they have links to terrorism and say they only learned of their no-fly status when they arrived at an airport and were blocked from boarding a flight.
The American Civil Liberties Union, which brought suit against the policy in 2010, argues that secrecy surrounding the list and lack of any reasonable opportunity for plaintiffs to fight their placement on it violates their clients' constitutional rights to due process.
The government contends there is an adequate means of contesting the flight ban and that individuals listed under the policy may ultimately petition a U.S. appeals court directly for relief.
The no-fly list, established in 2003 in the aftermath of the Sept. 11, 2001, attacks, bars those on it from flying within the United States or to and from the country.
As of last year, it included some 20,000 people deemed by the FBI as having, or reasonably suspected of having, ties to terrorism, an agency spokesman said at the time. About 500 of them were U.S. citizens.