Souques studied medicine in Paris, where in 1886 he became an interne and in 1891 earned his medical doctorate. Afterwards he worked as médecin des hôpitaux (Hospice de la Salpêtrière), and in 1918 became a member of the Académie de Médecine. With Joseph Babinski (1857-1932) and others he was a founding member of the Societé de Neurologie de Paris.
Souques is remembered for his extensive research of Parkinsonism, and in a 1921 treatise titled Rapport sur les syndromes parkinsoniens, he documented the importance of encephalitis lethargica as a cause of Parkinsonism. With his mentor Jean-Martin Charcot (1825-1893) he described the eponymous "Souques-Charcot geroderma", which is a variant of Hutchinson-Gilford disease. Souques is also credited with introducing the term "camptocormia" to describe an abnormal forward-flexed posture.