A medical official, who spoke to AFP on condition of anonymity, said 16 people, five of them soldiers, were wounded in the attack.
Hermel, in the Bekaa Valley where Hezbollah has a strong presence, has seen multiple attacks in recent months related to the war raging in neighbouring Syria.
The suicide car blast ripped through the checkpoint which lies at the entrance of Hermel, and at which cars are routinely stopped and searched by army troops.
Until today, the attacks had all killed civilians.
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The blast comes just four days after three people died in a twin bomb attack targeting the cultural centre of Hezbollah backer Iran.
And on February 1 a car bombing killed four people at a petrol station in Hermel, in an attack later claimed by Al-Nusra Front in Lebanon, a group named after Al-Qaeda's Syrian affiliate.
Extremist Sunnis see the army as taking the side of Hezbollah and other Assad allies in Lebanon's violence, which has escalated in recent months as a result of Syria's conflict.