Northern Iraq is a base for the outlawed separatist Kurdistan Workers' Party (PKK).
"Sixteen F-16 fighter jets took off from their base in Diyarbakir in the southeast at around 2000 GMT Tuesday and bombed the (rebel) targets in Qandil mountain in northern Iraq, 90 kilometres from the border," a military source said.
"More than 50 targets were hit in the three-hour operation."
Abdulrazzaq Bayiz, mayor of Senkasar region of Iraqi Kurdistan, confirmed the raid.
"Turkish aircraft targeted two villages in Senkasar at about 11 pm. They destroyed five houses in those villages. These attacks occurred over about 45 minutes, without any victims," he told AFP.
Bunker-busters developed by Turkey's Scientific and Technological Research Council(TUBITAK) were used for the first time in the raid, Turkish sources said.
The jets safely returned to their bases after the operation, they added.
Turkey says around 2,000 Kurdish rebels are hiding in the mountainous region on the Iraqi side of the border.
The PKK, listed as a terrorist group by Turkey and much of the international community, took up arms for autonomy in the Kurdish-majority southeast in 1984, sparking an insurgency which has claimed more than 40,000 lives.
The raids, the first in several weeks, come as the long-running conflict between the rebels and Turkey appears to reignite and threatens to derail peace talks between Ankara and jailed PKK leader Abdullah Ocalan with the aim of disarming the group.
Turkish Prime Minister Recep Tayyip Erdogan said Wednesday that the military operations against PKK bases would continue until the organisation laid down its arms.
"Our security forces will continue operations until the terrorist organisation lays down arms and ends its attacks," Erdogan said in televised remarks.
On Sunday, a senior PKK member was reported killed in a shootout in Turkey's Kurdish majority southeast, days after three women Kurdish activists were slain in Paris.
Turkish media reported last week that the weeks-long talks have produced a roadmap to end the three-decade-old Kurdish insurgency.
The reported roadmap has not been confirmed by either party.