Virginia Gamba, a UN representative on children in armed conflicts, signed an agreement with YPG's Mazloum Abdi to end child soldier recruitment. Turkey's foreign ministry said negotiating with a group with blood on its hands is unacceptable.
Turkey has lodged protests with the UN's Geneva office for signing a deal with the PKK terror group and with Switzerland for giving entry to terrorists.
The UN signed a deal with the SDF militia over the weekend, to end the recruitment of children for terrorist actions.
The PYD/YPG-dominated SDF militia has been used by the US to battle Daesh in Syria. The YPG is the Syrian offshoot of the PKK terror organisation.
Virginia Gamba, the UN secretary general's special representative on children in armed conflicts, met YPG militant Mazloum Abdi and signed the agreement over the weekend in Geneva.
There is a red notice warrant for Mazloum Abdi, whose real name is Ferhad Abdi Sahin.
"The UN’s confirmation that the terrorist organisation committed against children the gravest violations of international law and international humanitarian law, including the forceful recruitment, is important in terms of revealing once again the track record of the terrorist organisation in this regard," a press release from the Turkish foreign ministry said on Tuesday.
"It is, however, utterly unacceptable that the UN has taken a terrorist organisation with blood on its hands as an interlocutor to address this problem," the statement read.
In the PKK's 30-year terror campaign against the Turkish state more than 40,000 people, including women and children, have been killed.
Turkey, the US and the EU recognise the PKK as a terrorist organisation.
"There can be no explanation for the UN, which should be at the forefront in the fight against terrorism, to strike a deal with a terrorist organisation," the statement added.
The activities of the YPG-led SDF have been a major security concern for Ankara, while the US viewed the group as a "reliable partner" in the fight against Daesh, Ankara argues that the use of one terrorist group to counter another does not make any sense.