He joined the navy in 1939 as an officer candidate and became a midshipman (Fähnrich zur See) in November 1940. in April 1941 he was appointed watch officer on U-557 under Ottokar Paulshen and carried out three war patrols with her, from April to November 1941, during which he was involved in a number of engagements and took part in the sinking of five merchant ships.

Werner was promoted and sent to U-boat school for training, before joining U-612 in April 1942 as first watch officer under Paul Siegmann.

U-612 was lost accidentally in August 1942 while working up, although most of the crew were saved; they were transferred en bloc to U-230.

In April 1944 he took command of U-415 but made only two abortive sorties before she was sunk in harbour after detonating a mine.

Werner then took command of U-953, in August 1944 and escaped with her to Norway, from whence he made one unfruitful patrol before the German surrender in May 1945.