Stein arrived to India in December 1887, a country that was to remain his home for the rest of his life. Soon he was offered the joint posts of Principal of the Oriental College and Registrar of the Punjab University in Lahore. From the very beginning he felt comfortable in the British environment, partly due to three scholars he met upon his arrival at the capital of the Punjab who proved to be lifelong friends: the historian and classical scholar P. S. Allen (1869-1933), the Arabist Sir Thomas Walker Arnold (1864-1930) and Frederick Henry Andrews (1866-1957), who at that time was Principal of the Mayo School of Art. Andrews later became Stein’s assistant, dedicating long periods of his life to cataloguing Stein’s archaeological finds.

In the first decade of his career in India, Stein worked as a philologist. He collected Sanskrit manuscripts, and edited and translated the 12th century Kashmiri chronicle, the Rajatarangini. For the elucidation of the chronicle’s topographical details, his vacations were devoted to antiquarian research in Kashmir. Later, in the company of Andrews, he continued these short archaeological expeditions to neighbouring Kashmir, where he learnt the rudiments of photography from Andrews. This work prepared him for the long archaeological expeditions in Chinese Central Asia.

In 1899 he was appointed Principal to the Calcutta Madrasah, but held this post only for one year. His plans for exploration in Chinese Turkestan were now matured, and he had the necessary official support.