Four persons were injured in the incident that took place near Allah Dino Saand railway station. The engine driver and a fireman have been among the injured persons.
Two persons on board the ill-fated van said to be untraced so far.
According to railways officials, the engine was also damaged in the incident and was replaced. The train had been stopped at Allah Dino Saand station for the purpose. All passengers of the train have been safe.
Karachi’s railway link with the rest of country remained suspended for some hours due to the incident.
AFP reports: In the latest accident to hit the country’s run-down railways the northbound Fareed Express hit the van near Allah Dino Sand, a village 170 kilometres (105 miles) north of Karachi.
A Sindh provincial health official, Dr Hasan Murad Shah, said the dead and the injured in the accident Sunday night were from the same extended family of farmhands.
Railway accidents in Pakistan generally take place at the unmanned crossings. They lack barriers and sometimes signals, leaving commuters to judge for themselves whether it is safe to proceed.
At other times vehicles find themselves stuck on the tracks.
Train accidents are common in Pakistan, which inherited thousands of miles of track and trains from former colonial power Britain.
But the railways have seen decades of decline due to corruption, mismanagement and lack of investment.