During the Harsha`s period, Jain religion was prevalent at certain places in the northern India. Vaisali and Pundavardhan were the strong holds of Jainism. Jain religion was divided into two main sects such as Svaitamber and Digambar. However, Digambar sect was more prominent and attracted larger number of followers. Bana has also mentioned Jain religion in his books. According to Hiuen Tsang as compared to Buddhism, Jainism was more on the decline. Later on Jainism became more prevalent in southern India. Pulakasin II had extended his royal support and patronage to Jainism.

Thus it can be said that Harsha was tolerant towards other religion and followed a policy of religious toleration throughout his reign. His personality was the combination of different religions. It is true that he did more for the development of Buddhism but he had given religious freedom to his people and they were free to adopt any religion they liked.