The attack comes after reports of covert airstrikes carried out by Israeli forces at Iranian bases in the Jabal Azzan region south of Aleppo.
Syrian anti-aircraft defences shot down missiles that hit the Syrian air base of Shayrat in Homs province late Monday night, Syrian state television said.
Shayrat air base was targeted past year in a US cruise missile attack in response to a chemical attack that killed at least 70 people, including children, on the rebel-held town of Khan Sheikhoun.
State-run television showed images of an intercepted missile and called the attack an "aggression".
No country has yet claimed the attack after midnight but US officials recently said that Washington wasn't planning another strike after the missile strike on Saturday. Reports close to the regime indicated that its defences shot down six missiles targeting the base.
Damascus skies erupt with surface to air missile fire as the United States launches an attack on Syria targeting different parts of the Syrian capital Damascus, Syria, April 14, 2018. Most of the missiles were downed, a Syrian military official said.
A Hezbollah milita media unit shortly afterward stated that Syrian air defenses intercepted three missiles that targeted the Dumayr airport in northeast Damascus.
"There is no U.S. military activity in that area at this time", a Pentagon spokesman, Eric Pahon, said.
On 9 April, Israel targeted the Syrian Tiyan facility, also known as T4, killing several Iranian fighters.
Syria denied it was responsible for the attack, which killed at least 80 people.