The Panama-flagged ship carrying 10,000 toys and 10,000 packages of food and aid to be delivered to children in Gaza via the Israeli port of Ashdod.
The Turkish Red Crescent are putting efforts to swiftly transfer the aid and distribute to Gazans, the Social Affairs Ministry said.
The ship set sail Friday following reconciliation deal between Turkey and Israel after a six-year hiatus.
Turkey and Israel reached an initial reconciliation agreement last Monday. Diplomatic relations between the two countries were suspended after Israeli troops stormed a Gaza-bound aid ship called Mavi Marmara in international waters in 2010, killing 10 Turkish activists.
The Mavi Marmara aid ship was among six civilian vessels trying to break Israel's blockade of Gaza when Israeli commandos boarded it.
In the aftermath of the attack, Turkey demanded a formal apology from Israel, compensation for the families of those killed, and the lifting of Israel's Gaza blockade.
In 2013, Israeli Prime Minister Benjamin Netanyahu voiced regret for the attack.
Under the deal, in addition to agreeing to Turkey's humanitarian presence in Gaza, Israel will pay $20 million in compensation to the families of the Mavi Marmara victims.