Setting off from the port of Norfolk on the Virginia coast, the MV Cape Ray is due to arrive in the southern port of Gioia Tauro in about "two to three weeks," spokesman Colonel Steven Warren told reporters.
The 650-foot (197.5 meter) cargo ship has been outfitted with two large portable hydrolysis systems designed to neutralize lethal chemical agents in Syria's arsenal.
Defense Secretary Chuck Hagel sent a letter to Captain Rick Jordan and the 135-member crew telling them they were embarking on a "historic mission."
"You are about to accomplish something no one has tried," Hagel wrote in the letter released by the Defense Department.
"You will be destroying at sea one of the world's largest stockpiles of chemical weapons and helping make a safer world," he wrote.
The Cape Ray was initially supposed to head out earlier on Monday but engine problems delayed the scheduled departure, officials said.
The ship has a crew of 35 civilians operating the vessel and will have a 63-member team in charge of the hydrolysis units as well as a security force on board, AFP reported.
The hydrolysis machines will mix heated water and other chemicals to break down the lethal agents, resulting in a sludge equivalent to industrial toxic waste.
Last year, the UN Security Council last year backed a US-Russian deal to remove and destroy Syria's chemical arsenal.