The gunmen, armed with rocket-propelled grenades and rifles, attacked the checkpoints in the remote Chaambi Mountains in the southern region of the country on Wednesday.
The attacks come as thousands of Tunisian troops have been deployed to the area to fight the militants since April.
Tunisian News Agency said fourteen soldiers were killed and nine wounded when the heavily-armed militants assaulted the army base.
Since late 2012, Tunisian troops have been battling dozens of militants hiding out in the Chaambi Mountains . Eight soldiers were killed in an ambush last July.
The recent attack on military checkpoints comes during a period of relative calm in Tunisia, after a bloody 2013, with the authorities talking of an improved security situation in recent months while warning that the anti-terror struggle will be a long one.
More than 20 security personnel were reportedly killed in 2013 in what the government described as terrorism-related incidents. Two opposition politicians were also assassinated in 2013 in separate attacks that plunged the country into crisis.