Born in Prague, and raised in a German family in Bohemia (which at the time was part of the Habsburg monarchy), he served as a medical officer in the First World War.
After the war, he became a professor of the German Charles-Ferdinand University in Prague and director of the Kinderklinik (children's clinic).
He was the younger brother of Karl Hilgenreiner, a theologian and politician, also professor at Charles University.
As a professor at the Karls-Universität in Prague, he became a specialist on the diagnosis and cure of congenital luxation of the hip joint in infants and young children.
Heinrich Hilgenreiner (1935) "Die angeborene Dysplasie der Hüfte: 10 Jahre Abduktionsschiene und Frühbehandlung der angeborenen Hüftverrenkung" in: "Zeitschrift für orthopädische Chirurgie einschliesslich Heilgymnastik und Massage", Stuttgart, 63: 344-483.