Planning for the construction of the Global Vipassana Pagoda began in 1997, while actual building work started in 2000. The pagoda consists of three sub-domes. The first and largest dome was completed when bone relics of Gautama Buddha were enshrined in the central locking stone of the dome on October 29, 2006, making it the world's largest hollow stone masonry structure containing relics of the Buddha. The relics were originally found in Bhattiprolu, Guntur district, Andhra Pradesh, South India. They have been donated by the Mahabodhi Society of India and the Prime Minister of Sri Lanka to be kept at the Global Vipassana Pagoda. The second and third domes, along with an auxiliary dome adjoining the second dome, sit atop the first dome. Construction of the third dome was structurally completed on November 21, 2008.

The center of the Global Vipassana Pagoda contains the world's largest stone dome built without any supporting pillars. The height of the dome is approximately 29 metres, while the height of the building is 96.12 meters, which is twice the size of the previously largest hollow stone monument in the world, the Gol Gumbaz  Dome in Bijapur, India. The external diameter of the largest section of the dome is 97.46m and the shorter sections, is 94.82m. The internal diameter of the dome is 85.15m. The inside of the pagoda is hollow and serves as a very large meditation hall with an area covering more than 6000 sq m (65,000 sq ft). The massive inner dome seats over 8000 people, enabling them to practice the non-sectarian Vipassana meditation as taught by Mr S N Goenka, and now being practiced in over 160 centres in more than 60 countries. An inaugural one-day meditation course was held at the pagoda on December 21, 2008, with Mr S.N. Goenka in attendance as the teacher.

The aim of the pagoda complex is to express gratitude to Gautama Buddha for dispensing a universal teaching for the eradication of suffering, to reveal the truth about the life of Buddha and His teaching, and to provide a place for the practice of Vipassana meditation. Vipassana meditation courses are held free of charge at the meditation centre that is situated in the Global Vipassana Pagoda complex.