The son of a farm laborer from Saint-André d'Hebertot in France, Vauquelin began work as an apprentice to a Rouen apothecary. He became a laboratory assistant to Antoine-François Fourcroy (1783–91), with whom he later collaborated. Vauquelin became a member of the French Academy of Sciences in 1791 and professor of chemistry in the School of Mines in 1795. In 1799 he wrote Manuel de l'essayeur (An Assayer's Manual), which led to his being appointed assayer to the mint in 1802 and professor of chemistry at the University of Paris in 1809.

Vauquelin is best known for his discovery of the elements chromium and beryllium. In 1798, while working with a red lead mineral from Siberia known as crocolite, he isolated the new element chromium – so called because its compounds are very highly colored. Martin Klaproth made a similar discovery shortly afterward. In the same year Vauquelin also isolated a new element in the mineral beryl. It was initially called glucinum because of the sweetness of its compounds, but later given its modern name of beryllium. He was the first to isolate an amino acid: asparagine from asparagus.