"Earlier today a projectile fired from Syria hit the northern Israeli Golan Heights," an army statement said.
"No injuries have been reported."
There was no immediate report of an Israeli response.
On Tuesday Israeli aircraft struck Syrian army positions after stray fire from Syria's war hit the Israeli-occupied zone.
Syria said it had shot down an Israeli warplane and a drone, a claim denied by Israel.
Signup to our newsletter and follow us on Facebook and Twitter!
The uptick comes as a new Syrian ceasefire brokered by Russia and the United States came into force on Monday.
The truce does not apply to areas held by jihadists such as the Islamic State group.
The Israeli army holds the Syrian government accountable for any fire from its territory, regardless of its source.
There were similar events in July and previously.
Israel has sought to avoid being drawn into Syria's complex war which is now in its sixth year, but it has attacked Syrian military targets when fire from the conflict spills over.
Israel seized 1,200 square kilometres (460 square miles) of the Golan Heights from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.