The wheelchair racer suffered from an incurable degenerative muscle disease which left her in constant pain and caused seizures and paralysis in her legs.
She signed papers in 2008 allowing doctors to end her life at a chosen time. Euthanasia is legal in Belgium.
"On 22 October 2019, Marieke Vervoort, 'our Wielemie', passed away," read a statement from her home city of Diest. "Marieke opted for euthanasia a few years ago and responded to her choice on Tuesday evening."
Tokyo Skytree lights up in Paralympic colours for one-year countdown
Vervoort had previously said sport was her "medicine" and the knowledge she could end her own life eased her anguish. She won gold in the T52 100m and silver in the 200m at London 2012, before winning silver over 400m and bronze in the 100m at the Rio Paralympics four years later.
"If I didn’t have those [euthanasia] papers, I wouldn’t have been able to go into the Paralympics," she said in a 2016 interview. "I was a very depressed person – I was thinking about how I was going to kill myself. In England, I hope, and every country, they will look at euthanasia in another way – it’s not murder.
"With euthanasia, you are sure that you will have a soft, beautiful death, and that you can do it with the people you want who stay with you. It gives a feeling of peace and rest on my body that I can choose myself how far I will go."
Diest mayor Christophe De Graef added: "She always stayed in it to believe. Believe in performance, believe in being able to handle it. A goal every time capture. How difficult sometimes. Let it be a lesson for all of us. In perseverance, but also in perspective."
IPC suffering cashflow issues after Games postponement
Paralympic Games added to 'crowd jewels' list