Jessenius became physician in Carolinian University and personal physician of king Rudolf II. The plague stroke the town Prague. His healthy wife had been murdered throughout this time. He treated ill king Rudolf, and after his death, he embalmed him.

Jessenius had been dismissed by the new king Matthias. He spent next winter with woman Flora. After her death, he took care of their common daughter. He became rector of the Carolinian University. After Prague defenestration and outbreak of the Bohemian revolt, he had been appointed as a delegate of revolting side and got into Hungary.