Khunrath was born in Dresden, Saxony, the son of the merchant Sebastian Kunrat and his wife Anna in the year 1560.
Khunrath, a disciple of Paracelsus, practiced medicine in Dresden, Magdeburg, and Hamburg and may have held a professorial position in Leipzig.
He travelled widely after 1588, including a stay at the Imperial court in Prague, home to the mystically-inclined Rudolf II, Holy Roman Emperor.
Khunrath's brushes with John Dee and Thölde and Paracelsian beliefs led him to develop a Christianized natural magic, seeking to find the secret prima materia that would lead man into eternal wisdom.
John Warwick Montgomery has pointed out that Johann Arndt (1555–1621), who was the influential writer of Lutheran books of pietiesm and devotion, composed a commentary on Amphitheatrum.
Khunrath may have encountered some opposition to his alchemical work because most of his publications on alchemy were published widely after his death.