Sirens warning of incoming rockets sounded in the Golan Heights on Sunday afternoon, but security forces initially said there were no impacts in Israeli territory.
The alarms came hours after a false alarm in southern Israel, outside the Gaza Strip.
Fighting on the Syrian side of the border between rival rebel groups has been inching closer to the Israeli border, with many cases of errant mortar fire falling in Israel.
Unlike in the Gaza Strip, the IDF generally avoids firing back at Syrian territory.
Last week, Druze residents of Majdal Shams in the Golan Heights attacked an IDF ambulance and killed a wounded Syrian man.
Their coreligionists in Syria, who are allies of the Bashar Assad regime, have been besieged by Islamist rebels in recent weeks.