Nest Te Kōhanga, the zoo's animal hospital and centre for native wildlife, performed an endoscopy on the native bird and removed the vape pen.
Sadly the Shag died overnight.
"A sad reminder to please always tidy up after yourself and make sure these lovely birds don't mistake your rubbish for food."
The team at Nest Te Kōhanga believe the Shag wouldn't have eaten for days and could have suffered from "serious metal and nicotine poisoning".
Although this is the first time the Wellington Zoo has come across an animal swallowing a vape pen they said they come across "these sorts of problems regularly".