In August 1752, Gouan received his doctorate under the chairmanship of Antoine Magnol (1676–1759), and subsequently practiced medicine at Saint-Éloi Hospital in Montpellier.

In 1762 Gouan published a plant catalog of the botanical garden at Montpellier titled Hortus regius Monspeliensis.

In 1770 he published an important ichthyological treatise called Historia Piscicum, a work that expanded the number of fish genera that existed in the Linnaean system.

During his career he maintained correspondence with several learned scientists and thinkers, which included in addition to Linnaeus; Albrecht von Haller (1708–1777), Jean Guillaume Bruguière (1750–1798), Jean-Jacques Rousseau (1712–1778), Carl Peter Thunberg (1743–1828), et al. One of his students in Montpellier was Jacques Anselme Dorthès.

Gouan is credited with planting the first ginkgo biloba in France, a tree that was given to him by naturalist Pierre Marie Auguste Broussonet (1761–1807).