It is the third baby monkey death at the zoo since 2008.
The female monkey's body was discovered by a zoo attendant on the morning of May 12, as the zoo was preparing Mother's Day celebrations for its mother, April.
The cause of death of the baby, which still hadn't been named, has not yet been determined. The body has been sent to Fredericton for a necropsy to be conducted. The results are expected later this week.
The Callimico goeldii is one of the rarest primates on Earth, though scientists are unsure how many remain.
Lynda Collrin, director of zoo development and a primatologist, says the baby's death is devastating for both the staff and the survival of the species.
"This would be a new founder's blood line and to lose that, it's so important, every baby born and any new blood line made is so important for this species, for its survival," she said.
The baby, born at the zoo on March 9, weighing only about one ounce, had just begun to run around and eat solid foods, Collrin said.
"Everything was going so well," she said. "So it was totally unexpected. I just have no answers."
Mother had been kidnapped in 2008
It was the first baby for April, who was kidnapped from the zoo five years ago.
April was nine months old when she was snatched from the facility. She was discovered three days later in a blue plastic box in the Bayside Drive area after the Saint John Police received an anonymous tip.
Although zoo staff had been unsure how that trauma would affect April as a mother, she was "amazing," Collrin had said.
April's brother, Charlie, however, had become overly protective following the kidnapping and zoo officials blamed his overprotective tendencies for the two previous baby monkey deaths.
Charlie was trying to protect the babies and would keep them from their mother, preventing them from getting enough nourishment, officials had said.
Charlie has since been sent to another zoo, leaving no answers but many questions around the latest death.
Meanwhile, the zoo is hoping April and her mate will have another baby by the end of the year.