Harlaftis obtained an undergraduate degree in physics at the University of Athens in 1987, and a Ph.D. degree at the University of Oxford in 1991, under the supervision of Phil A. Charles. His thesis title was Disc structure and variability in dwarf novae. From 1991 to 1995 he worked as a support astronomer at the Isaac Newton Group of telescopes of the Royal Greenwich Observatory, placed at the Observatory of Roque de los Muchachos (owned by the Instituto de Astrofisica de Canarias at the island of La Palma. He then worked as a research assistant (1995-1997) at the University of St. Andrews and as a research fellow (1997-1998) at the Institute of Astronomy and Astrophysics of the National Observatory of Athens, where he was appointed to a position of a tenure track researcher in 1999. He held a series of posts as a visiting scientist at the University of Sheffield, and the NASA Goddard Space Flight Center (1999), and two years as a temporary Reader at the School of Physics and Astronomy at the University of St. Andrews (2001-2002). He acted as a principal investigator for the Aristarchos 2.3 m Telescope located at the Chelmos mountain, which colleagues suggested to name after him, following his death in an avalanche accident.