Her death came within weeks of her brother's. He died from the rare genetic disease three days before Christmas last year.
Batten's disease is a progressive disorder which causes blindness, deafness and loss of muscle control. It is usually fatal by the age of 10.
It is understood that Charly's funeral will be on Friday, the day before her parents are due to host a charity Valentine's Ball at the Hilton Hotel in London.
A number of celebrities - including Pauline Quirke and Samantha Janus - who support the Rhys Daniels Trust are expected to attend.
Double tragedy
The children's parents, Barry and Carmen Daniels, have campaigned tirelessly to help other sufferers of Batten's disease. They also have a healthy three-year-old daughter called Bliss.
Rhys was the first child to have a bone-marrow transplant to try to cure the genetic disease in 1993.
His case came to national attention when his parents went to the High Court in London over the closure of the hospital where he was being treated.
He eventually underwent two transplants in Bristol but both failed. His condition slowly worsened until he was unable to walk, stand, see or speak and had to be fed through a tube.
Charly's condition was detected too late for the same life-saving surgery to be attempted.
In September 1997 the family announced they would not subject either child to further painful treatments and would simply let nature take its course.
'They suffered enough'
At the time Mr Daniels said: "Rhys and Charly have suffered enough. We don't want to put them through any more.
"We've talked it over and have decided that next time they fall ill or get an infection we don't want them rushed to hospital to have needles stuck in them.
"We want them here at home where we can give them our love and let them die peacefully."
Mrs Daniels has described how Charly had "always looked so content".
"We were devastated to learn that Charly, then aged three, would never grow up to be a teenager, buy records or ride on the bus with friends." she said.