Guru Harkrishan was born on July 7, 1656 to Guru Har Rai and Krishan Kaur. Before his death in October 1661 Guru Har Rai had appointed his younger son Harkrishan as the next Guru as opposed to his elder son Ram Rai who was in collusion with the mughals. Guru Harkrishan was only five years old when he received the guruship.

The Gurus older brother Ram Rai complained to emperor Aurengzeb in Delhi that he had been discriminated against because of his loyalty to the emperor and had not received his due share of the property of his father Guru Har Rai. Ram Rai knew that before his death Guru Har Rai had instructed Guru Harkrishan to never meet Aurengzeb. Ram Rai hoped if Guru Harkrishan met the emperor he would be going against his fathers wishes and the Sikhs would be displeased with their Guru. On the other hand if Guru Harkrishan refused to come to Delhi, then he would be attacked by the emperors forces.

Since Aurengzeb was very friendly with Ram Rai he summoned Guru Harkrishan to appear before him in Delhi. The Sikhs were very apprehensive about allowing young Guru Harkrishan to go to Delhi. Aurengzeb sent Raja Jai Singh a high court official known for his devotion to the Gurus to escort the Guru to Delhi.

Raja Jai Singh assured the Guru that he would not have to meet the emperor personally while in Delhi, and that there were a large number of devotees in Delhi who were anxious to see and hear their Guru. Guru Harkrishan convinced the Sikhs at Kiratpur that he should go to Delhi. As a result Guru Harkrishan along with his mother and a group of devotees set out for the long journey to Delhi. On their journey the Guru was met by large crowds of devotees. At Panjolhara an jealous Brahmin taunted the Guru, "Your Guru is called Hari Krishna, a mere child of eight years! Krishna, the incarnation of Vishnu, uttered the Gita which is the repository of all the eternal truths, If your Guru also calls himself Krishna, let him expound the truths of Gita to us". Hearing this a poor watercarrier called Chhajju stood up and proclaimed that anyone could expound on the Gita if he were so blessed by the Guru. Guru Harkrishan touched Chhajju with his walking stick and Chhajju immediately began explaining the philosophy of the Gita. The Brahmin was so humbled by the spectacle that he fell to the Gurus feet and asked forgiveness for his arrogance.

Upon reaching Delhi the Guru and his party were the guests of Raja Jai Singh who had promised to uphold the safety of the Guru. Every day large numbers of devotees started flocking to see the Guru. At this time a smallpox epidemic was raging in Delhi. The Guru helped to heal many sick people, naturally coming in contact with so many people every day, the Guru was also infected and taken seriously ill. On March 30, 1664 Guru Harkrishan decided to announce his successor, the Guru 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". Guru Harkrishan then suddenly passed away at the tender age of eight years old.