The raid was the fourth strike against PKK bases inside Iraq since Friday's ambush which killed 15 soldiers, prompting the most intense fighting between Turkish troops and Kurdish fighters in eight months.
The military said troops fought back, killing at least 23 rebels, but that two soldiers were still missing after the attack.
Turkey accuses the PKK of using the region as a sanctuary from where to plan and carry out deadly attacks against Turkish troops in the south and eastern regions of Turkey.
Troops and rebels have regularly exchanged fire in the border regions in recent months.
Ankara blames the PKK for a series of attacks on Turkish targets, notably a series of blasts in Istanbul in July.
More than 40,000 people are thought to have been killed since 1984, when the PKK launched its campaign for a Kurdish homeland in southeastern Turkey.