Thapa was admitted to Medanta Hospital in Gurgaon on March 29. He was a post bypass surgery patient.
He died last night at 10.44 pm and his body was taken away by his family members at 10.40 am today, a senior doctor at the hospital said.
"He was admitted with weakness and chest infection and subsequently was diagnosed to have cancer of the stomach. He was operated on April 10.
"He showed some improvement after that but later developed some complications including irregular heat beats," the doctor said.
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Thapa served as Nepal's Prime Minister three times before 1990. After multi-party democracy was established in 1990, he formed the Rastriya Prajatantra Party and held the post of Prime Minister twice. He stepped down in 2005. He was the oldest member of Nepal's Constituent Assembly which is currently drafting a constitution.
"His body will be flown to Nepal's capital Kathmandu, for cremation on Friday," said Thakur Sharma, a spokesman for Thapa's Rastriya Prajatantra Party.
Thapa is survived by his son and three daughters. His son, Sunil Bahadur Thapa, is Nepal's commerce and supply minister. His wife had died few years ago.