Sectarian violence has been on the rise in Pakistan, where hardline Sunni militant groups have been relentlessly attacking Shias whom they see as heretics.
The first explosion took place metres away from a Shia mosque near a busy market in Parachinar, capital of the tribal Kurram area. It was followed shortly afterwards by a second blast, close to another mosque in the town.
Riaz Mahsud, the top administrator of the Kurram region, said 39 were killed and 72 wounded, adding that the attacks were carried out by suicide bombers on motorbikes.
"Some of the injured are still in critical condition and have been shifted to the main hospital in Parachinar," he said.
It was unclear which group carried out the attack and no one immediately claimed responsibility. Shia Muslims make up a little over 10 per cent of Pakistan's population of 180 million.
Parachinar itself is home to a significant Shia community which has been previously targeted by Sunni militants.
Pakistan has suffered a spate of bombings since Prime Minister Nawaz Sharif was sworn in last month, underscoring the challenges he faces in taming sectarian violence as well as an escalating Taliban-linked insurgency.
Sabir Hussain, a doctor at the Agency Headquarters Hospital, earlier said 15 bodies and 45 people with serious wounds had been brought to his hospital.
Both explosions took place before sunset just as people flocked to the market area to buy food for their evening meals after a day of fasting during the holy month of Ramzan. "A lot of people usually throng roadside markets in Parachinar before sunset for Iftar (dinner) shopping," said tribesman Haider Ali. "Hundreds of people were present during the blasts and that's why the death toll was high."