In a statement the army said the "intensive" bombing targeted a large cave in the Qandil mountains along the Iraqi-Iranian border, where up to 40 PKK fighters were taking refuge.
"The cave was completely destroyed and most of the militants who were inside and outside the cave were rendered ineffective," it said.
A second PKK target, in the Zap region along the Turkish border, was also bombed, the statement said, without giving further details.
Zap and the Qandil mountains are both major PKK strongholds.
PKK denial
Ahmed Deniz, a PKK spokesman in northern Iraq, denied that the Turkish bombing had not caused any casualties or serious damage despite lasting for around one hour.
Firat News, a pro-Kurdish news agency, said the bombing was immediately followed by shelling by neighbouring Iranian forces.
An official of the autonomous Kurdish administration in northern Iraq told the AFP news agency that the Kali Birdan area of the Qandil mountains had been the target of Turkish air raids on Tuesday and that villages had been hit.
"Turkish planes bombed the villages near Kali Birdan, where there are only families who earn their living raising sheep," Sinksar Abdullah, director of the region, said.
Two bomb blasts in a crowded Istanbul street on Sunday evening killed 17 people, among them five children, and left more than 150 wounded.
Turkish media reports have said that a PKK fighter trained in the Qandil mountains is suspected of having carried out the attacks.
"The police, who have established a description of the terrorist ... are working on the presumption that he came alone from the Qandil mountains," the Vatan newspaper reported on Tuesday.
Ongoing offensive
The PKK, which is listed as a terrorist group by Ankara, the European Union and the United States, has denied responsibility for the blasts.
Turkish fighter jets have been bombing PKK positions in the mountains of northern Iraq since December 16.
In February, the army conducted a week-long ground offensive against PKK bases in the region, in the which the army said it had killed at least 240 fighters and destroyed dozens of hideouts, training camps and ammunition depots.
Turkey estimates that more than 2,000 fighters have taken refuge in Kurdish-run northern Iraq, using camps there as a jumping board for attacks on Turkish targets across the border.
The Turkish government has a one-year parliamentary authorisation for cross-border military action against the PKK, which expires in October.
The United States has backed its Nato ally by providing real-time intelligence on PKK movements in Iraq.
The PKK took up arms for self-rule in Turkey's mainly Kurdish southeast in 1984, sparking a conflict that has claimed more than 37,000 lives.