During the 1880s, Moissan focused on fluorine chemistry and especially the production of fluorine itself. The existence of the element had been well known for many years, but all attempts to isolate it had failed, and some experimenters had died in the attempt.
He had no laboratory of his own, but borrowed lab space from others, including Charles Friedel. There he had access to a strong battery consisting of 90 Bunsen cells which made it possible to observe a gas produced by the electrolysis of molten arsenic trichloride; the gas was reabsorbed by the arsenic trichloride.
Moissan eventually succeeded in isolating fluorine in 1886 by the electrolysis of a solution of potassium hydrogen difluoride (KHF) in liquid hydrogen fluoride (HF).  The mixture was necessary because hydrogen fluoride is a nonconductor. The device was built with platinum-iridium electrodes in a platinum holder and  the apparatus was cooled to −50 °C. The result was the complete separation of the hydrogen produced at the negative electrode from the fluorine produced at the positive one, first achieved on 26 June 1886. This remains the current standard method for commercial fluorine production. The French Academy of Science sent three representatives, Marcellin Berthelot, Henri Debray, and Edmond Frémy, to verify the results, but Moissan was unable to reproduce them, owing to the absence from the hydrogen fluoride of traces of potassium fluoride present in the previous experiments. After resolving the problem and demonstrating the production of fluorine several times, he was awarded a prize of 10,000 francs. For the first successful isolation, he was awarded the 1906 Nobel Prize in Chemistry. Following his grand achievement, his research focused on characterizing fluorine's chemistry. He discovered numerous fluorine compounds, such as (together with Paul Lebeau) sulfur hexafluoride in 1901.