Police said the 53-year-old Oamaru woman, who was not wearing a seat belt, received minor to moderate injuries when she was thrown around in the van during the crash, about 9.30am.
She was treated for her injuries at Oamaru Hospital and later discharged.
Nearby residents spoken to by the Otago Daily Times did not see the crash, but heard the train and "a big bang".
They thought the train had hit something, and when they came out, the van was lying on the west side of the tracks.
The train stopped about 350m north, near the Caledonian Rd crossing, and did not appear to have received any major damage.
It was going to the Alliance Group's Pukeuri works with two wagons of coal.
Toll Rail's corporate affairs general manager Sue Foley said the train driver, travelling north, saw the van approaching the level crossing, gave a lengthy blast on the train's horn and applied the emergency brakes.
The train clipped the rear of the van, throwing it down a small bank to the side of the tracks.
The woman driver was "really, really lucky" not to be seriously injured, she said.
The crossing had "passive" controls - warning and stop signs - but no alarms or barriers.
"It reinforces that people need to be aware a train can come through at any time.
It is no different from an intersection - take care to make sure nothing is coming before crossing," she said.
The train driver declined to comment when approached by the Otago Daily Times.
Acting Sergeant Ross Lory, of Oamaru, said police were still investigating the crash, but charges were likely to be laid.
The courier van was travelling west and failed to stop at compulsory stop signs at the railway crossing, driving in front of the train, which hit the rear of the vehicle.
Freightways' contractor for Oamaru, Noel Murray, yesterday brought another van from Timaru to Oamaru to replace the one damaged - "what's left of it", he said.
"It was lucky the driver also wasn't a write-off," he said.
Mr Murray said the driver told him she did not see the train until too late, driving up the hump approaching the railway line.
He said the driver was "quite good" yesterday, but had received bruising and a twisted knee in the crash.
