Meitner's earliest research began at age eight, when she kept a notebook of her records underneath her pillow. She was particularly drawn to mathematics and science, and first studied colours of an oil slick, thin films, and reflected light. Women were not allowed to attend public institutions of higher education in Vienna until 1897, and she completed her final year of school in 1892. Her education included bookkeeping, arithmetic, history, geography, science, French and gymnastics.
The only career available to women was teaching, so she trained as a French teacher. Her sister Gisela passed the Matura, and entered medical school in 1900. In 1899, Meitner began taking private lessons with two other young women, cramming the missing eight years of secondary education into just two. Physics was taught by Arthur Szarvasy. In July 1901, the girls sat an external examination at the Akademisches Gymnasium. Only four out of fourteen girls passed, including Meitner and Henriette Boltzmann, the daughter of physicist Ludwig Boltzmann.
Meitner entered the University of Vienna in October 1901. She was particularly inspired by Boltzmann, and was said to often speak with contagious enthusiasm of his lectures. Her dissertation was supervised by Franz Exner and his assistant Hans Benndorf. Her thesis, titled  ("Examination of a Maxwell Formula"), was submitted on 20 November 1905 and approved on 28 November. She was examined orally by Exner and Boltzmann on 19 December, and her doctorate was awarded on 1 February 1906. She became the second woman to earn a doctoral degree in physics at the University of Vienna, after Olga Steindler who had received her degree in 1903; the third was Selma Freud, who worked in the same laboratory as Meitner, and received her doctorate later in 1906. Meitner's thesis was published as  ("Thermal Conduction in Inhomogeneous Bodies") on 22 February 1906.
Paul Ehrenfest asked her to investigate an article on optics by Lord Rayleigh that detailed an experiment that produced results that Rayleigh had been unable to explain. She was not only able to explain what was going on; she went further and made predictions based on her explanation, and then verified them experimentally, demonstrating her ability to carry out independent and unsupervised research.
While engaged in this research, Meitner was introduced by Stefan Meyer to radioactivity, then a very new field of study. She started with alpha particles. In her experiments with collimators and metal foil, she found that scattering in a beam of alpha particles increased with the atomic mass of the metal atoms. Later on, this led Ernest Rutherford to predict the nuclear atom. She submitted her findings to the Physikalische Zeitschrift on 29 June 1907.