Canterbury District Health Board medical officer of health Ramon Pink yesterday confirmed the baby died of the disease in Christchurch Hospital last month.
The baby, who was born prematurely, had been scheduled to go to Auckland's Starship children's hospital but had been too sick to travel.
"It was a very difficult experience for [the family]," Pink said.
One other pertussis death has been reported this year. It involved a 3-year-old unimmunised child with underlying health conditions from another part of the country.
"It's a tragic reminder, I think, of the seriousness of whooping cough. It's a significant issue and showing no signs of abating. It is a national epidemic," Pink said.
About 5389 cases of whooping cough, also known as pertussis, have been reported throughout the country this year, including 1150 in Canterbury and 52 involving children under 1.