At least 10 people were wounded, with two in critical condition, as the strike hit positions in Qusaya near Lebanon's border with Syria, said Anwar Raja of the Popular Front for the Liberation of Palestine-General Command.
Israel has denied involvement in the assault.
The PFLP-GC has positions along the Lebanon-Syria border, as well as a military presence in both countries.
The group has carried out attacks against Israel in the past.
The reported assault come as tensions heighten between Israel and Hezbollah.
“An old rocket exploded in an arms depot on the base and five fighters were killed,” a security source told AFP.
The group has close ties with the Syrian government and its main Lebanese ally Hezbollah. It has bases in Lebanon's eastern Bekaa Valley as well as in Al Naameh, just south of Beirut.
The Israeli military told Reuters that it does not comment on reports in foreign media.
“There was no Israeli attack on the PFLP along the Lebanon-Syria border,” reported a correspondent for Israel's army radio, citing officials.