The ministry said the attack occurred late on Thursday as the soldiers were carrying out road checks in northern Syria, in an area that is under the control of Turkish forces and Turkish-backed Syrian fighters since a Turkish incursion into the region in October.
"Three heroic brothers-in-arms were martyred in a car-bomb attack during a road check," the ministry said. It did not provide further details on the attack.
No group immediately claimed responsibility for the bombing.
Turkey invaded the border area in neighboring Syria to drive away the Syrian Kurdish People's Protection Units, or YPG, a group it considers terrorist because of its links to Kurdish rebels fighting inside Turkey. However, the same fighters were the main U.S. allies on the ground in the war against the Islamic State group.
Thursday's blast was the latest in a series of attacks targeting Turkish troops or the allied Syrian rebels in northern Syria. Four soldiers were killed last week in a similar car bomb explosion.
More than 20 Turkish soldiers have died in the region since the start of the incursion, which drew widespread international criticism. The United States in turn was seen as abandoning the Syrian Kurdish force that had helped fight IS militants.