Eman Abd El Aty, said to have weighed around 500kg (1,102lb), left an Indian hospital on Thursday after doctors said she lost more than 250kg.
She flew business class to the United Arab Emirates. Doctors say she will undergo a year of physiotherapy there.
Recent weeks saw a row erupt between her doctors in India and her family.
It began when her sister, Shaimaa Selim, released a short video on social media alleging that her sister was still unable to speak or move, and had not lost as much weight as the hospital was claiming.
The hospital strongly denied the allegations.
The surgeon, Dr Muffi Lakdawala, told an Indian news channel that Ms Selim had wanted her sister to stay in hospital until she was able to walk again, but orthopaedic specialists had told her Ms Abd El Aty would never walk again.
Doctors, paramedics and nurses accompanied her on the passenger flight to Abu Dhabi, according to reports.
She had arrived in India on a specially-modified Airbus plane in February and was put on a special liquid diet to reduce her weight so that doctors could perform bariatric surgery.
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