The 5-year-old passed away at Faridpur Medical College Hospital on Monday evening, his father Lablu Shikder told bdnews24.com.
He said they took him to the state-run Magura General Hospital after Sunday midnight after his abdomen swelled.
He was transferred to the medical college hospital later when his condition deteriorated. He died around 6:30pm.
He will be buried at his village Khalia on Tuesday, Lablu said.
A board of doctors at the Magura General Hospital checked him and sent him to Dhaka for better treatment after media reported his condition in May last year, but his condition worsened.
The news also drew huge attention of the international media at the time.
He was later undergoing treatment by Dr Debashish Biswas, a doctor at the Magura General Hospital.
Dr Biswas said Bayezid needed a surgery as the sagging skin blocked his urination passage.
But the doctor said he could not conduct the surgery considering it risky for other conditions.