Stoltenberg said the strikes by the United States, France and Britain were a "clear message" to the head of the regime, Bashar Assad, to Russian Federation and Iran that the use of chemical weapons is not acceptable and that the allies would not stand by and watch.
Stoltenberg also thanked Turkey for the support in the air operations in Syria.
"We will never have a total guarantee against new attacks as long as we have regimes which are willing to use chemical weapons", he said.
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"There were efforts for an independent investigation into the alleged use of chemical weapons in Syria but Russian Federation prevented it", Stoltenberg said. Syria has denied responsibility, but the U.S., France and Britain have said there is no doubt the Assad government was responsible.
"That's a national decision for a North Atlantic Treaty Organisation country".
After he was welcomed by a military ceremony at the Defense Ministry, Stoltenberg met with Defense Minister Nurettin Canikli.
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The NATO chief is also set to meet on April 16 with President Recep Tayyip Erdoğan and Foreign Minister Mevlüt Çavuşoğlu during his visit, state-run Anadolu Agency reported.
The U.S., United Kingdom and France "coalition" launched a very precise attack "on reported Assad regime chemical weapons facilities in Syria", in the early hours of last Saturday.
On April 7, more than 40 civilians were killed in a suspected chemical attack in Douma outside Damascus.
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Russian Federation has also used its United Nations veto six times to prevent condemnation of Assad's use of chemical weapons. He said the analysis was done at the request of the Organization for the Prohibition of Chemical Weapons.