Doctors initially attempted to x-ray the suspected abuse victim, but nothing confirmed her injuries.
Eventually a team of five doctors operated and found the rolling pin inside her intestines.
The husband and wife, both from Nepal, had come to the hospital together.
Dr Kedar Singh Shahi, a general surgeon at the hospital, said: "We were very shocked. We did not expect anything like this.
"We could only see a shadow in the x-ray as wooden materials cannot be identified.
"The internal damage she suffered was very serious and she could have died.
"The size of the rolling pin was around 40cm long which is a big size to be inserted into a human body."
The woman was hesitant to explain what had happened, prompting the hospital authorities to inform the police and the National Commission for Women (NCW).
Amita Lokhani, vice-chairperson of NCW, said: 'The matter came to me a day after the operation.
"The woman was in a terrible condition when I first visited her. She was not only in pain but terrified to speak to anyone.
"I tried asking her what had happened but she did not say a word and kept crying.
"Her husband was present at the time.
"I continued visiting her for three days and eventually she opened up on the third day while her husband was away.
"She told me she was infertile and her husband often tortured her.'
Senior Superintendent Janmejaya Khanduri, of Nainital Police, said the man was on the run charged with rape and grievous bodily harm with a team of officers hunting for him.
The woman is being treated free of cost at the hospital and is likely to be discharged next week and the NCW will continue to counsel her.
Dr Shahi added: "She came to us in a very poor state affected badly with septicemia. Her life was in grave danger but she is currently doing well and we're positive she will make a recovery."
"She's been a very brave lady."