Turkey's state-run media, the Anadolu news agency quoting government sources, said that US Embassy Charge d'Affaires Phillip Kosnett was summoned to the ministry.
The YPG is the main element in a force that Washington has assisted with training, weapons, air support and help from ground advisers in the battle against ISIS.
Turkey's Foreign Minister Mevlut Cavusoglu said that relations with the United States were harmed by Washington's refusal to extradite cleric Fetullah Gulen and its provision of arms to the Kurdish militant YPG.
Turkey's foreign ministry has summoned a senior U.S. diplomat to express Ankara's "discomfort" over Washington's support for Syrian Kurdish fighters, state media reported.
Wednesday's move was not the first time Turkey has expressed displeasure with the USA about the issue.
In October, the YPG and their allies announced the capture of ISIL's self-declared capital of Raqqa in Syria after a four-month operation. The Turkish Foreign Minister Mevlut Cavusoglu also called out Russian Federation and Iran to stick to the joint accord they signed with Turkey a year ago agreeing on a "de-escalation zone" in Idlib which were set up to scale back the conflict.
Turkey on Wednesday called on Russian Federation and Iran, the two chief allies of President Bashar al-Assad's regime in Syria, to halt an air offensive on the rebel-held Idlib province near the Turkish border. The reports say that Syrian government forces, supported by Russian Federation were trying to regain control of areas controlled by Daesh and other rebel groups.
Cavusoglu said that ties between the North Atlantic Treaty Organisation allies could be harmed further if Washington does not correct its mistakes, Reuters reported.
Russia, Iran and Turkey are supposed to be the guarantors of last year's accord but Moscow and Tehran appear bent on reneging on their role to de-escalate fighting in the area, home to almost 2 million Syrians, to serve their own agenda.
Cavusoglu claimed about 95 percent of all violations of the joint accord were carried out by the regime and the groups backing the regime.