The legal move by the Hon. Susan J. Crawford upholds President Obama's Guantanamo order to halt court proceedings at the Navy detention center in Cuba.
The military charges against suspected Al Qaeda bomber Abd al-Rahim al-Nashiri marked the last active war crimes case at Guantanamo Bay.
Pentagon spokesman Geoff Morrell said Crawford dismissed the charges against al-Nashiri without prejudice. That means new charges can be brought again later. He will remain in prison for the time being.
"It was her decision, but it reflects the fact that the president has issued an executive order which mandates that the military commissions be halted, pending the outcome of several reviews of our operations down at Guantanamo," Morrell said Thursday night.
The ruling also gives the White House time to review the legal cases of all 245 terror suspects held there and decide whether they should be prosecuted in the U.S. or released to other nations.
Retired U.S. Navy Cmdr. Kirk Lippold, who was commander of the USS Cole when it was attacked in Yemeni waters in 2000, told FOX News that he was invited to the White House on Friday for a special meeting with Obama.
Lippold decried Obama's request to delay all pending trials at Guantanamo. But he told FOX News he "will go with an open mind and wait to see and hear what President Obama has to offer."
FOX News' Catherine Herridge and the Associated Press contributed to this report.