"The PKK must become involved in political and parliamentary life instead of resorting to weapons, since using guns does wrong to Kurds and Iraqis."
Ankara has previously accused Baghdad of not doing enough to halt PKK attacks, and has launched a number of air raids on alleged Kurdish fighter positions in northern Iraq.
Gul said on Monday that the time had come "to end all these problems which hinder relations between Turkey and Iraq".
"A thorough operation must be carried out [against the PKK], and this is the responsibility of all of us."
The Turkish president was also scheduled to meet the prime minister of Kurdistan, Iraq's autonomous northern province.
Ahmed Deniss, a spokesman for the PKK, claimed the aim of Gul visit's was to "liquidate" the group.
"Turkey and the United States have a plan to disarm the PKK and liquidate it. They want the complicity of the Iraqi Kurdish government," he told the AFP news agency.
Turkey, Iraq and the United States agreed last January to set up a joint command centre to gather and share intelligence on the PKK.
The PKK, labelled a terrorist group by much of the international community, took up arms for self-rule in Turkey's Kurdish-majority southeast in 1984. Ankara blames the group for the up to 44,000 lives that have been claimed in the conflict since them.