Separatist Baloch militants on Tuesday blew up the railway track and hurled rockets at the Jaffar Express when it was on its way to Peshawar in Khyber Pakhtunkhwa province from Balochistan's capital of Quetta, a security source said.
The military's spokesperson Ahmed Sharif Chaudhry said 21 hostages and all 33 insurgents had been killed. He said 440 people had been on board.
"Today we freed a large number of people, including women and children ... The final operation was carried out with great care," Chaudhry said on Wednesday, adding that no civilians were killed in the operation.
He said the security forces had cleared the train "bogey to bogey".
The Baloch Liberation Army, which claimed the attack, is the largest of several ethnic armed groups battling the government in Balochistan, which borders Afghanistan and Iran.
The militants have in recent months stepped up their activities using new tactics to inflict high death and injury tolls and target Pakistan's military.
Baloch militant groups say they have been fighting for a larger share in the regional wealth of mines and minerals.
On Wednesday evening, before the army announcement, the BLA said it had killed 50 passengers.
The BLA had threatened to start executing hostages unless authorities met its 48-hour deadline for the release of Baloch political prisoners, activists, and missing people it says were abducted by the military.
A junior government minister had earlier said 70-80 attackers had hijacked the train.
