It was unclear if the missile caused any damage or injuries. Israel's military said it was fired toward the Israeli community of Avivim, but did not immediately give further details.
A military spokesman also called on Israelis living within four kilometres (2.5 miles) of the Lebanese border to remain at home and prepare shelters, though it did not call on them to enter the shelters for now.
Tensions have risen in the last week between Israel and its enemy Hezbollah, the Lebanese Shiite movement backed by Iran.
Hezbollah chief Hassan Nasrallah said Saturday the group's response to the alleged Israeli drone attack on the group's Beirut stronghold had been "decided".
The pre-dawn August 25 attack involved two drones -- one exploded and caused damage to a Hezbollah-run media centre and another crashed without detonating due to technical failure.
Israel has not claimed responsibility for the incident.
The attack in Lebanon came just hours after Israel launched strikes in neighbouring Syria to prevent what it said was an impending Iranian drone attack on the Jewish state.