Police said the nine-month-old twins were in a "serious but stable" condition after being hurt while sleeping in their cots on Saturday night.
Officers and paramedics were called to a house in Homerton, east London, after reports the animal had attacked the pair.
The girls were being treated at the Royal London Hospital. They both reportedly suffered arm wounds and one was reported to have facial injuries.
The fox was believed to have been in an upstairs room.
A Scotland Yard spokesman said: "The incident is not being treated as suspicious. We were called to reports of a fox attack. Officers and the ambulance found two girls with injuries."