Its army, which is backed by the United States, has begun a fresh offensive which is targeting extremists in the settlements of Ras Baalbek and Qaa.
Lebanese commander Joseph Aoun announced the operation - which comes after steady successes against IS over the past year - via Twitter and the Central Military Media outlet.
President of Lebanon Michel Aoun, who is of no relation to the Lebanese commander, arrived at the defence ministry on Saturday to monitor the situation.
Simultaneously, the Syrian army and the Lebanese Hezbollah group have revealed a similar campaign to rid IS from the Qalamoun mountains on the Syrian side of the border.
The two county's state military forces are co-operating, though Lebanese authorities insist they are not co-ordinating with the government of Syria's President Bashar Assad.
Towns and villages on the Lebanon/Syria border have experienced shellings and kidnappings, while car bombs made there have been used to deadly effect in other parts of Lebanon.
The area was overrun by militants linked to al-Qaeda and IS in 2014, which led to the kidnapping of Lebanese soldiers.
Politicians in Lebanon say around 115 square miles of land between the two countries is currently controlled by IS. Around half of the territory is on the Lebanese side of the border.
The area also includes the Lebanese town of Arsal and sections of the western Syrian town of Qusair.