Along with Hrachia Ajarian and Manuk Abeghian, Stepanos Malkhasiants was a key name in Armenian philology of the first half of the twentieth century.

He was born in Akhaltskha (Akhaltsikh), Javakhk, nowadays in Georgia, on November 7, 1859. He received his primary education at the Karapetian parochial school in Akhaltskha and then the local Russian gymnasium. From 1874 to 1878 he attended the Gevorgian Seminary in Vagharshapat. Malkhasiants was later admitted to the department of Oriental Studies at St. Petersburg State University and graduated in 1889 with an emphasis in Armenian, Sanskrit, and Georgian Studies and a first doctorate in philology.