A contemporary Jesuit account, written by Spanish Jesuit missionary Jerome Xavier (1549–1617), who was in Lahore at the time, records that the Sikhs tried to get Jahangir to substitute the torture and death sentence to a heavy fine, but this attempt failed. Dabistan-i Mazahib Mobad states Jahangir tortured Guru Arjan in the hopes of extracting the money and public repudiation of his spiritual convictions, but the Guru refused and was executed. Jerome Xavier, in appreciation of the courage of Guru Arjun, wrote back to Lisbon, that Guru Arjan suffered and was tormented.

Arjan was born in Goindval to Bibi Bhani and Jetha Sodhi. Bibi Bhani was the daughter of Guru Amar Das, and her husband Jetha Sodhi later came to be known as Guru Ram Das. Arjan's birthplace site is now memorialized as the Gurdwara Chaubara Sahib. He had two brothers: Prithi Chand and Mahadev. Various Sikh chroniclers give his birth year as 1553 or 1563, the latter is accepted by scholarly consensus as the actual year of birth with 15 April as the accepted birth date.

The mainstream Sikh tradition recognised Guru Arjan as the fifth Guru, and Hargobind as the sixth Guru. Arjan, at age 18, became the fifth Guru in 1581 inheriting the title from his father. After his execution by the Officials of the Mughal Empire for attempting to hinder with the Mughal succession of ruler. After him, the Sikh Gurus were hereditary, as his son Hargobind became the sixth Guru in 1606 CE and later the title of Guru remained within the family.

The Akbarnama by Abu'l-Fazl Allami mentions that Guru Arjan met the Mughal Emperor Akbar and his cortege in 1598. According to Louis Fenech, this meeting likely influenced the development of Sikh manuscriptology and the later martial tradition.

One of the Sikh community disputes following Guru Ram Das was the emergence of new hymns claiming to have been composed by Nanak. According to faction led by Guru Arjan, these hymns were distorted and fake, with some blaming Prithi Chand and his Sikh faction for having composed and circulated them. The concern and the possibility of wrong propaganda, immoral teachings and inauthentic Gurbani led Guru Arjan to initiate a major effort to collect, study, approve and compile a written official scripture, and this he called Adi Granth, the first edition of the Sikh scripture by 1604.

In 1606 CE, the Guru was imprisoned in Lahore Fort, where by some accounts he was tortured and executed, and by other accounts the method of his death remains unresolved. Shaikh Ahmad Sirhindi cheered the punishment and execution of Guru Arjun, calling the Sikh Guru an infidel.

Some scholars state that the evidence is unclear whether his death was due to execution, torture or forced drowning in the Ravi river. J.S. Grewal notes that Sikh sources from the seventeenth and eighteenth century contain contradictory reports of Guru Arjan's death. J. F. Richard states that Jahangir was persistently hostile to popularly venerated non-Islamic religious figures, not just Sikhism. Bhai Gurdas was a contemporary of Guru Arjan and is a noted 17th-century Sikh chronicler. His eyewitness account recorded Guru Arjan life, and the order by Emperor Jahangir to torture the Guru to death.