His father was Peter Handlirsch (1831–1873) and mother was Rosina Handlirsch (born 1841). His father worked as a cook of the Schwarzenberg family. His surname Handlirsch came from Czech: handlíř "merchant".
Initially a pharmacist, Handlirsch became an assistant to Friedrich Moritz Brauer in the department of entomology of the Natural History Museum of Vienna in 1892. He became the director of this department in 1922, a function which he held until his retirement. He specialised in the Hymenoptera and the Hemiptera, his work concerning the evolution of these and other insects. His principal work, which appeared between 1906 and 1908, was on insect fossils and he was the founder of insect palaentology. The University of Graz gave him the title of Doctor of Science honoris causa and he was made a member of the Academy of Science of Vienna. He is best known for Die Fossilen Insekten (1906–1908) – 1,433 pages and 51 plates – and his contributions to the third volume of Christoph Schröder's Handbuch der Entomologie (1920–1925) – 1,201 pages with 1,040 figures. Handlirsch's fossil collection is mostly in the Naturhistorisches Museum in Vienna. Other parts are in the Ernst-Moritz-Universität in Greifswald.
- Guido Nonveiller (2001). Pioneers of the Research on the Insects of Dalmatia. Croatian Natural History Museum (Zagreb) : 390 p.
- Evenhuis, N. L. 1997 Litteratura taxonomica dipterorum (1758-1930) Leiden, Backhuys.
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