Safa and Marwa Bibi underwent three major operations, spending more than 50 hours in theatre.
Their mother, Zainab Bibi, told the BBC she was delighted to be taking them back to the rest of their family.
"The girls are doing very well. Marwa has made good progress and only needs a little support," she said.
"We will keep an eye on Safa and take good care of her. God willing, both will start walking."
Conjoined twins are rare, and of these only one set in 20 are born joined at the head, with a fused skull - what's known as craniopagus twins. The vast majority do not survive beyond childhood.
A team of 100 people at Great Ormond Street Hospital (GOSH) was involved in their care.
The twins were separated in February 2019, and since then have been living with their mother and uncle in London. All their medical and other costs - more than £1 million - were paid for by a private donor, Pakistani businessman Murtaza Lakhani.
But he told the BBC he still had some misgivings about the outcome.
"I feel Marwa has done really well and carries on making great progress. When I look at the whole family, yes, it was probably the right thing to do, but for Safa as an individual I'm not so sure."
Mr Jeelani, a hugely experienced neurosurgeon, is still troubled by the near-impossible choice he and his team had to make in theatre.