Edward Flatau was born on December 25, 1868 in Płock (which in the 19th century was in the Russian Empire) as one of five children of a banker and grain merchant Ludwik and his wife Helena nee Heyman. In childhood he was seriously ill with typhoid fever. For a long time he was unconscious, and (as he mentioned years later) after the illness he had a much better and sharper memory. This incident was the basis for the later theory of Flatau, that infections may have a positive influence on the nervous tissues. In 1886 Flatau finished with a gold medal at Płock middle school – the oldest and one of the best schools in the Polish land. In the same Year he moved to Moscow and started to study medicine. During the study, Flatau contacted with two distinguished Russian scientist: neurologist Aleksei Kozhevnikov and psychiatrist Sergei Korsakoff. It can be expected that these scientists had a big influence on the later scientific interests of Flatau.

Flatau got a medical degree with honors in 1892. After the graduation, he went to Berlin to improve his knowledge concerning the neuroanatomy and neurology. During his stay in Germany, Falatau co-worked with world class specialists in this area, including Emanuel Mendel, Ernst Viktor von Leyden, Hermann Oppenheim, Hugo Liepmann and others. At that time Flatau developed his independent scientific activity. At the age of 26 (two years after study), Flatau got publicity by publishing “Atlas of the human brain and the course of the nerve-fibres”.

The atlas presented in detail the surface, cross-sections and anatomical relationships in the fresh brain using long-exposure photos made with a specially constructed camera. Photographs were made in the department of prof. Emmanuel Mendel.

This was the first such precise description of the brain anatomy. In the words of Sigmund Freud, “The photographs in the atlas were clear and accounted for excellent educational material”. The work of Flatau gained international fame and shortly it was translated into German, English, French, Russian, and in 1896 into Polish. In 1899 Flatau published the second edition of the atlas which was extended and composed of two parts: an atlas and a supplement.

Flatau was a supporter of women’s emancipation, because as he wrote in the work “The nervous system in the light of newest studies”: “If we want to stay in the field of facts and do not draw unilateral and subjective conclusions, then we must say that the data taken from the anatomy and concerning the weight of the female brain cannot serve as a weapon against the higher aspirants of women”.

In Germany Flatau also worked on the histology of the nervous system. He was a strong supporter of the neuron theory, introduced (together with the term "neuron") by Wilhelm Waldeyer to describe the basic structural unit of the nervous system in 1891. Flatau argued the oneness of the neuron by the transection of Oculomotor nerve in dogs and observation of changes in its nuclei. Then he together with Alfred Goldscheider also studied the influence of various pathological stimuli (mechanical, thermal and toxic) on anatomy and functions of neuronal cells. The observations obtained during the study were presented in the book “Normal and pathological anatomy of nerve cells" published in 1898.

Simultaneously Flatau conducted numerous experiments on dogs, during which he transversely cut spinal cords, acted on the spinal cords using electrical stimuli and observed symptoms. On the basis of these experiments he noted that "greater the length of the fibres in the spinal cord the closer they are situated to the periphery" and this statement is known as Flatau's law.

The obtained results Flatau described in the work entitled  “The law of excentric storage of long tracks in the spinal cord” published in 1897, which was the basis to receive a PhD in medical sciences in Moscow in 1899. The famous neurologist Louis Jacobsohn-Lask said about this work: “Among the many works which Flatau announced at the time, one especially impressed me because it was a simple and happy solution to the problem of building a part of the nervous system”. During his stay in Germany Flatau also wrote books about comparative anatomy of the nervous system in mammals and athological anatomy of the nervous system, as well as he was the author of the chapter about inflammation of the peripheral nerves in the famous, classic manual of pathology of Nothnagel.

Thanks to his academic work, Flatau became famous around the world. In 1898 he obtained a proposition form the university in Buenos Aires to be a chair of the Department of Neurology, but Flatau felt Polish and wanted to work in Polish lands.