The Otago Sparks player sustained a partial ligament rupture in the elbow during the team's training camp in Dubai ahead of this year's Women's 50 over World Cup and managed the injury throughout the tournament.
The recovery timeline meant she would not be available for the rest of the home summer season and the ICC Women's T20 World Cup in England and Wales in June and July.
As the injury affected her bowling arm, head coach Ben Sawyer said they had opted for surgery.
"We're all really gutted for Eden. The team has a big six months ahead and I know how difficult it was for her to make the decision to go through with the surgery now, but I fully support it.
"It'll obviously be a huge loss for the team not having Eden available - especially for the T20 World Cup where she played a big role for us last year.
"At just 24 years old she's still got a long career ahead, so it's important we look forward and prioritise getting her back on the park and fully fit."
New Zealand would next host Zimbabwe in February and March for three T20s and three one-day internationals in Hamilton, Wellington and Dunedin.
