Born at Lorch (Württemberg), Hafenreffer was professor at Tübingen from 1592 until his death in 1617.
He was a motivating teacher with a charismatic influence upon his students.
He combined strict faithfulness to the Book of Concord with a peaceful disposition.
Among those who enjoyed his instruction and correspondence was the astronomer Johannes Kepler.
His chief work was his system of doctrine under the title Loci Theologici (1600).