One of the missiles hit a shop and other landed near a mosque in Shungak area in the remote Parachinar in Kurram Agency. Two other missiles hit a graveyard in Kachkina area.
The residents were panicked after the shop was destroyed in Shingak area. No incidents of loss of life were reported, authorities said.
An official said the missiles were fired from Afghanistan's Paktia province.
Kurram, which borders three Afghan provinces, is one of the most sensitive tribal areas.
The incident occurred in the same area where the Pakistani Taliban on Friday targeted a Shiite imambargah with a powerful car bomb, killing at least 24 people and injuring nearly 100 others at a crowded market.