Honoré Fabri entered the Jesuit Order in 1626 spending two years at Avignon. In 1628 he entered the Collège de la Trinité in Lyon where he studied philosophy, going on to study theology at Lyon from 1632 to 1636. He was ordained in 1635.
His first position was in a Jesuit college, namely as professor of philosophy in Arles from 1636 to 1638. Further positions in Jesuit colleges followed. He was professor of logic in Aix- en- Provence for a year from 1638 then, for six years from 1640, professor of logic and mathematics at the Collège de la Trinité in Lyon.