At a news conference with Turkish Foreign Minister Ahmet Davutoglu, Mr Kerry said the two Nato allies shared a common goal - to end the suffering of innocent civilians in Syria.
Turkey and the US both oppose Syrian President Bashar al-Assad, but differ on how best to support the opposition.
The visit has been overshadowed by the Turkish PM's remarks about Zionism.
Recep Tayyip Erdogan earlier this week called Zionism a "crime against humanity" - remarks that have been widely condemned,