Charles Moureu attended school in Bayonne. At 17, he apprenticed with his older brother, Félix Moureu, in his brother's pharmacy in Biarritz, in preparation for studies in pharmacy.
From 1884 to 1891 Moureu studied at the École Supérieure de Pharmacie in Paris. He received the school's silver medal in 1886, and both its gold medal and the Laillet Prize in 1887.
In addition, he interned in the Hôpitaux de Paris from 1886 to 1891, where he was given first place rank of the interns in 1887 and in 1889.
Moureu received a degree in 1888 and graduated as a pharmacist first class in 1891, whereupon he was given a position as chief pharmacist of the public asylum of the Seine (des Asiles de la Seine). He remained in this position from 1891 to 1907. This allowed him to continue his research, studying organic chemistry with  and Charles Friedel. He received his doctorate in physical sciences in 1893 from the Sorbonne, with the dissertation Contribution à létude de lacide acrylique et de ses dérivés (Contribution to the study of acrylic acid and its derivatives).
He obtained his agrégation in 1899.