About 60 militants crossed over from Afghanistan and attacked the Pakistani army post in the Ghakhi area of the Bajur tribal region when the soldiers were having pre-dawn Ramadan meal before fasting.
A security official said the rebels came from Kunar province of Afghanistan.
"Two soldiers and a captain were killed in the attack," he said.
Another solider and a civilian cook were also injured.
In retaliatory fire, the troops injured several attackers who escaped to Afghanistan after the gun battle.
Fazlullah fled to Afghanistan in 2009 after his group was routed in a military operation in Swat area of Khyber- Pakhtunkhwa province.
In June, militants killed 20 soldiers in three attacks.
Pakistani forces killed about 50 attackers in retaliatory attacks.
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