Czochralski was born in Kcynia, West Prussia (now in Poland). Around 1900 he moved to Berlin, where he worked at a pharmacy. He was educated at Charlottenburg Polytechnic in Berlin, where he specialized in metal chemistry. Czochralski began working as an engineer for Allgemeine Elektrizitäts Gesellschaft (AEG) in 1907.
He discovered the Czochralski method in 1916, when he accidentally dipped his pen into a crucible of molten tin rather than his inkwell. He immediately pulled his pen out to discover that a thin thread of solidified metal was hanging from the nib. The nib was replaced by a capillary, and Czochralski varified that the crystallized metal was a single crystal. The experiments of Czochralski produced single crystals that were a millimeter in diameter and up to 150 centimeters long. Czochralski published a paper on his discovery in 1918 in the Zeitschrift für Physikalische Chemie, a German chemistry journal, under the title "Ein neues Verfahren zur Messung des Kristallisationsgeschwindigkeit der Metalle" [A new method for the measurement of the crystallization rate of metals], since the method was at that time used for measuring the crystallization rate of metals such as tin, zinc and lead. In 1950, Americans G.K. Teal and J.B. Little from Bell Labs used this method to grow single germanium crystals, which begans its use in producing suitable semiconductors.
In 1917, Czochralski organized the research lab "Metallbank und Metallurgische Gesellschaft", which directed until 1928. In 1919 he was one of the founding members of the German Society for Metals Science (Deutsche Gesellschaft für Metallkunde), of which he was president of in 1925. In 1928, at the request of the president of Poland, Ignacy Moscicki, he moved to Poland and became the Professor of Metallurgy and Metal Research in the Chemistry Department of the Technical University in Warsaw.
After World War II he was stripped of his professorship due to his involvement with Germany during the war, although he was later cleared of any wrongdoing by a Polish court. He returned to his native town of Kcynia where he ran a small cosmetics and household chemicals firm until his death in 1953.