Harkrishan was born on July 7, 1656, to Guru Har Rai and Krishan Kaur.

Before his death in October 1661, Guru Har Rai appointed him the next guru in preference to his elder son Ram Rai, who was in collusion with the Mughals.

Ram Rai complained to Emperor Aurangzeb in Delhi that he had been discriminated against because of his loyalty to him. He knew that before his death, his father had instructed Harkrishan to never meet Aurangzeb. He hoped that if the meeting took place the Sikhs would be displeased with their guru.

On the other hand, if Harkrishan refused to come to Delhi, the emperor would be infuriated and order his troops to seize the guru.

Since Aurangzeb was well disposed towards Ram Rai, he summoned Guru Harkrishan.

The Sikhs were very apprehensive about allowing their guru, who was only a boy, to go to Delhi. So Aurangzeb sent Raja Jai Singh, a high court official known for his devotion to the gurus, to escort him to Delhi.

Raja Jai Singh convinced Guru Harkrishan to visit the emperor. In Delhi the guru and his party were Raja Jai Singh's guests.

At this time a smallpox epidemic was raging in Delhi. The guru helped to heal many sick people, but in the process got infected himself.

On March 30, 1664, Guru Harkrishan decided to announce his successor. He called for five coins and a coconut. He took them and being too weak to move, waved his hand three times in the air and said, 'Baba Bakala!'

He passed away at the tender age of eight.