The incident happened in Spinwarm area of North Waziristan where the Pakistani military on June 15 launched the major offensive to drive out local and foreign militants from the region.
A security official said that the blast occurred 100 metres from a security post when the vehicle was stopped by Pakistani troops.
"A nearby building collapsed after the explosion, killing two soldiers and one civilian," said the official.
It is not immediately known how many militants were there in the vehicle.
The offensive against militants in North Waziristan bordering Afghanistan was launched a week after the Taliban brazenly attacked the Karachi airport.
Pakistan has asked Afghanistan to plug its side of the border to stop militants from fleeing to sanctuaries there.