The surgery on the skull of one-year-old Roona Begum was carried out on Tuesday near New Delhi by the same surgeons who last week drained fluid from the youngster in a life-saving operation.
"We did the crucial head reconstruction surgery to reduce the size of her head on Tuesday. As of now, there are no complications," neurosurgeon Sandeep Vaishya told AFP.
The procedure involved shifting and cutting bone and tissue parts and at least one more round of surgery will be required, according to Vaishya.
He said the baby's health had "shown remarkable improvement" after last week's surgery at the hospital run by the private Fortis Healthcare group.
During the first operation, doctors used a surgical drill to pierce her skull before draining fluid from her head in an operation lasting more than an hour.
Roona was born with hydrocephalus, a condition that causes cerebrospinal fluid to build up on the brain. Her condition had caused her head to swell to a circumference of 94 centimetres (38 inches), putting pressure on her brain and making it impossible for her to sit upright or crawl.
She lives in an Indian village with her parents who were too poor to pay for treatment.
But publication of pictures taken by an AFP photographer in the remote northeastern state of Tripura prompted the hospital to offer to treat Roona for free.
The pictures of Roona have prompted an outpouring of support worldwide with prospective donors contacting AFP and other news organisations, enquiring how they could contribute to a fund for her and her family's welfare.
Two Norwegian college students, Jonas Borchgrevink and Nathalie Krantz, started an online campaign that raised $52,000 to help her family and fund any future aftercare.
The students told AFP they have already established contact with a local media website in Tripura that will help send the money to the family.
The website for donations can be viewed at www.mygoodact.com/collectiondetailperson.php?id=212.