The white-domed golden stupa - the country's largest and one of the holiest sites of pilgrimage in Tibetan Buddhism - was left with deep cracks after the powerful 7.8-magnitude quake hit in April last year, devastating the Himalayan nation and killing nearly 9,000 people.
Restoration work began in May 2015 and cost USD 2.1 million - including over 30 kilogrammes of gold - according to the Boudhanath Area Development Committee.
To mark the opening, which took place after a three-day purification ritual, colourful prayer flags and flowers covered the stupa and monks chanted prayers.
The UNESCO world heritage site, believed to have been built in the 5th century, was restored with donations from devotees and from Buddhist organisations around the world.
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"I am here almost everyday and was heartbroken to see it damaged after the quake. But it is now open to us, I am very happy to see it standing tall," said 66-year-old Dawa Lama who had come to the stupa to offer prayers.
Thangka artist Hom Bahadur Tamang, who has sold his Buddhist paintings in the stupa grounds for 21 years, said business had been slow.
"The reconstruction of the stupa has given us new hopes that we will rise again," Tamang said.
While work has begun to repair quake-damaged temples and monuments, only a handful have been completed, with experts saying it will be years before Nepal's architectural heritage is fully restored.
Meanwhile, many of the millions left homeless by the quake are facing a second winter without proper shelter because they have still not received the compensation money they need to start rebuilding their homes.