An animal welfare officer spotted the dead doe lying on a road near Cromer, Norfolk, last week.
When he saw its stomach still moving, he grabbed a knife from his vehicle and removed the female fawn.
While initially signs looked good for its survival, it took a turn for the worse earlier this week.
"It's been very distressing," said the investigator, who wishes to remain anonymous.
"We're all upset. We put a lot of effort in to try and save it and it's not nice when something like this does happen."
Following the Caesarean in the middle of the night, the fawn was taken to the Hillside Animal Sanctuary in Frettenham to be checked-over and given medication.
It then lived at the home of its rescuer where it was regularly fed and monitored.
But because it was born about a month early, the investigator said it was never certain whether it would live for long and it died on Wednesday.
"It was premature and perhaps it was also affected by the impact on its mum," said the investigator.
"The circumstances were extraordinary. We put all our efforts in and unfortunately it didn't win the battle."
A muntjac fawn saved by a quick-thinking motorist who carried out a roadside Caesarean on its dead mother has died.