Both deaths involved an employee of HWE Mining, the mining contractor that was acquired by Leighton Contractors in late 2005 and operates the Yandi mine.
BHP Billiton spokeswoman Samantha Evans told reporters that the latest fatality occurred on Thursday, involving a collision between a light vehicle and a haul truck.
Evans said police and other emergency services were immediately notified.
She said production at all of the company's large iron ore mines in the Pilbara region, which include Mt Whaleback and Mining Area C, had been temporarily suspended because management wanted to focus on safety.
"Safety comes before production," Evans said.
"We're concerned that incidents such as this may distract employees' attention away from the task, which could put them at risk.
"So by suspending operations, we can reduce the risks associated with that."
She said staff had been offered counselling.
The WA Department of Consumer and Employment Protection's resources safety division are heading to the mine and police say a coronial investigation is underway.
BHP Billiton said in a statement on its website that "our immediate priorities are the welfare of the family of the deceased and other people involved in the incident".
While it is the second death at Yandi, 140km north east of Newman, in two weeks it is also the third death at a BHP Billiton mine in WA in two months.
The third BHP Billiton death occurred at its Nelson Point Port Operations at Port Hedland on July 29.
Source: AAP NewsWire