The base located south of Beirut is operated by the Popular Front for the Liberation of Palestine-General Command, a small, Syrian-backed group that has been waging a decades long fight against the Jewish state.
"This is in response to the firing of projectile rockets last night toward Israeli communities," the military said.
It said it views such attacks with "extreme severity" and holds Lebanon responsible.
Maj. Gen. Udi Adam, head of the Israeli army's northern command, which oversees the tense Israel-Lebanon border, spoke hours after Katyusha rockets fired from Lebanon landed in the Israeli town of Kiryat Shmona. He said the army will retaliate to rocket fire by Lebanese militant groups.
"We will not allow Katyusha fire to become a routine of daily life, absolutely not," Adam told Israel's Army Radio. Israel ended an 18-year occupation of southern Lebanon in May 2000.
Witnesses reported warplanes roared over the PFLP-GC guerrilla base at Naameh, a hilltop base overlooking the Mediterranean five miles south of Beirut, and the sound of two booms were heard.
Other witnesses said two air-to-surface missiles were fired and white smoke billowed from the ground.
Police had no immediate confirmation of an airstrike, but Lebanese troops at a checkpoint near Naameh confirmed an air raid and sealed off the area, preventing journalists from approaching.
It was not immediately clear if there were any casualties from the raid on the target, a maze of concrete fortified tunnels built inside a hill that the PFLP-GC had used as a base for decades.
The airstrike was launched after three rockets landed in a residential area of Kiryat Shemona. The Israeli army said the rockets damaged some property but caused no injuries.
There was no immediate claim of responsibility for the attack. Both Hezbollah guerrillas and Palestinian militants operate in nearby southern Lebanon.
The raid came a month after Israeli jets attacked a command post of the Hezbollah guerrilla group in south Lebanon, responding to Hezbollah rocket and mortar attacks that wounded 11 Israeli soldiers and damaged a house in a border community.
Israel withdrew from an occupied enclave in southern Lebanon in 2000. While fighting in the area has dropped since then, the border remains tense and Hezbollah frequently targets Israeli troops in the disputed Chebaa Farms area.
Lebanon and Syria say Chebaa Farms is Lebanese territory, but U.N. cartographers who surveyed the border after the Israeli withdrawal said it belongs to that part of Syria which Israel has occupied since the 1967 Arab-Israeli war. Israel says it will discuss control of the area only in future peace talks with Syria.