The flotilla was formed in December 1938 in Kiel under the command of Korvettenkapitän Hans-Rudolf Rösing. It was named in honour of Oberleutnant zur See Hans Joachim Emsmann, a U-boat commander during World War I, who died on 28 October 1918 after his U-boat UB-116 was sunk by a mine. The flotilla was disbanded in January 1940 and the boats were all transferred to 1st Flotilla.