Barsha, one of the conjoined twins separated at Bangabandhu Sheikh Mujib Medical University (BSMMU) on Wednesday, died at the hospital about seven and a half hours after the operation.
Doctors said the baby could not stand the trauma of the seven-hour-long surgical operation.
Bonya, the other twin, is still kept in the neo-natal Intensive Care Unit (ICU) of the hospital and is not out of danger, the doctors said, adding that they are closely monitoring her condition round the clock.
"She has some temperature and pain because of the long operation," BSMMU's Paediatric Surgery Department Chairman Dr Shafiqul Haque told The Daily Star.
Shahnaz Begum, the twins' mother, lost consciousness several times following her daughter's death.
"You know how hard we have tried to save our children. We were aware of the risks of the surgery, yet it is very difficult to accept a daughter's death," the girls' father Golam Kibria, a schoolteacher of Dumurgachha Primary School in Gaibandha, told The Daily Star.
"We would do everything to save the other child," he said.
Six teams of 68 members including over 40 doctors took part in the surgery to separate the twins aged four months and 12 days. The twins were conjoined at their livers, intestines and gallbladders, chest bones and abdomen.
The babies regained consciousness soon after the surgery and were kept at the ICU. Barsha had to be given ventilation support for breathing problem.
"Barsha's blood pressure started going down at 10:00pm. The girl died at 11:20pm," Dr Shafiq said.
Receiving Barsha's dead body in the morning, the family buried her at their family graveyard in Rampura village of Gobindaganj upazila in Gaibandha after the Asr prayers yesterday.
The twins were born at Rabeya Clinic in Gaibandha on March 24 and were transferred to Dhaka Medical College Hospital the next day. They had been undergoing treatment at BSMMU since April 4 under Dr Shafiq's supervision.
Talking on Bonya's condition, Dr Ruhul Amin, associate professor of paediatric surgery at BSMMU, said, "We cannot say anything before five days." Dr Ruhul separated a pair of conjoined twins at Islami Bank Hospital in 2003 and one of the twins has survived.