During the Vedic and earlier Buddhist period "Ayurveda" was at its pinnacle. Ashoka also boosted up the contemporary Indian medicine by his official authority. Starting from the Maurya period the repeated Scythian invasions into India, Indian science suffered a lot. The research on Ayurveda gradually ceased to occur when the Turkish invaders came to India; it suffered further more.

When the Muslim rule in India became stable in the later Middle Ages, religious discrimination affected Ayurveda as a science of the Kafirs (non-believers of Islam). It is said Bakhtiyar Khalji destroyed thousands of books of the Nalanda University Library written on palm leaves. He also burnt the Vikramshila University which was located near modern Bhagalpur. The library of Vikramshila was also destroyed. The earlier Muslim rulers imported Unani physicians from their homeland. Some prudent Indian scholars spirited away valuable Indian texts to Tibet and China some of which are still extant.

During the Mughal period, particularly during the reign of Akbar, attempts at the reintroduction of Ayurveda were made which though very meagre still helped Ayurveda to live for the posterity. With entry of the Portuguese into India in the 15th century and later the British settlement of India during and after the reign of Jahangir, Ayurveda gradually eclipsed from the scene of India. From the 18th century onwards European medicine or Allopathy boarded the stage of Indian medicine.

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