He was the son of Simon Maccabaeus and hence the nephew of Judas Maccabaeus, Jonathan Maccabaeus and their siblings, whose story is told in the deuterocanonical books of 1 Maccabees and 2 Maccabees, and in the Talmud. John was not present at a banquet at which his father and his two brothers were murdered, purportedly by his brother-in-law Ptolemy. He attained to his father's former offices, that of high priest and king (although some Jews never accepted any of the Hasmoneans as being legitimate kings, as they were not lineal descendants of David).

John Hyrcanus apparently combined an energetic and able style of leadership with the zeal of his forebears. He was known as a brave and brilliant military leader. He is credited with the forced conversion of the Idumeans to Judaism, which was unusual for a Jewish leader; Judaism was not typically spread by the sword. He also set out to resolve forcibly the religious dispute between the Jews and the Samaritans; during his reign he destroyed the Samaritan temple on Mount Gerizim (although their descendants still worship among its ruins), which served further to deepen the already-historic hatred and rivalry between the two groups. Many historians believe that the apocryphal book of Jubilees was written during his reign; some would suggest even at his behest. Some writers, particularly Christian ones, have dated the division of Judaism into the parties of Pharisees and Sadducees to his era; most Jewish writers and some Christian ones suggest that this split actually well predates him. Some historians would go so far as to identify him, as a priest, predominantly with the Sadducee party, which was closely associated with the Temple worship and the priestly class.

John Hyrcanus represented in some ways the highest point of the Hasmonean Kingdom. The restored Jewish "kingdom" approached its maximum limits of both territory and prestige. Upon his death, his offices were divided among his heirs; his son Aristobulus succeeded him as high priest; his wife as "Queen regnant". The son, however, soon came to desire the essentially unchecked power of his father; he shortly ordered his mother and his brothers imprisoned. This event seems to mark the beginning of the decline of the Hasmonean Dynasty; in just over four decades they were removed from power by the Roman Republic and none of them ever began to approach the level of power or prestige that had pertained to John Hyrcanus or his predecessors.