Lecoq de Boisbaudran was a member of a noble family of Huguenots from the French provinces of Poitou and Angoumois. The Huguenots were French Protestants, a population that was devastated during the French Wars of Religion (1561–1598). The Edict of Nantes (1598) granted substantial civil rights to the Huguenots even though it maintained Catholicism's position as the established religion of France.  The Edict of Nantes was overturned by the Edict of Fontainebleau (1685), which officially sanctioned persecution of Protestants. The Lecoq de Boisbaudran family was of considerable fortune until the revocation of the Edict of Nantes, after which much of their property was confiscated and sold.
Paul-Émile (Francois) Lecoq de Boisbaudran was a son of Paul Lecoq de Boisbaudran (1801–1870) and his wife Anne Louise. Paul Lecoq de Boisbaudran established a successful wine business in Cognac, benefiting from the hard work of the entire family including young Paul-Émile.
Anne Louise Lecoq de Boisbaudran was well educated and taught her son Paul-Émile history and foreign languages, including English. He obtained the syllabus of the École Polytechnique, and he studied the books assigned in its courses. In this way, he was self-taught as a scientist. As such, de Boisbaudran is an example of an autodidact. With the support of his family, he assembled a modest chemical laboratory on the second floor of their home on the Rue de Lusignan. In this laboratory, he repeated the experiments that he had studied in books. Through these experiments, he developed his theories of spectroscopy and made most of his discoveries, including the isolation of gallium.
Lecoq de Boisbaudran married Jeannette Nadault-Valette (1852–1926) on 27 December 1897. They had no children. He developed ankylosis of the joints, and failing health hindered his work after 1895. He died in 1912, at the age of 74.