Eisenkot did his military service in the Golani Brigade, of which he became commander in 1997–98. He served as a soldier, a squad leader and a platoon leader. In the First Lebanon War he served as a Company commander in the Golani brigade. During the South Lebanon conflict (1985–2000) he served as the brigade's Operations Officer and as the commander of the Golani Orev Company. Later, he served as Golani's 13th Battalion commander, the Deputy to the Commander of the Brigade and an operations officer of the Northern Command. Afterwards he served as Carmeli Brigade's commander and as the commander of the Ephraim Brigade. In 1997 he replaced Col. Erez Gerstein and was appointed commander of the Golani Brigade. During that time Eizenkot led the brigade in a series of operations in southern Lebanon that resulted 40 Hezbollah operatives killed.