The boat was built by Kaiserliche Werft Danzig and was launched on 27 March 1909.

On 17 January 1911, U-3 sank near Kiel harbour in Heikendorfer Bay because of an unclosed ventilation shaft valve.

Its entire 30-man crew was rescued by SMS Vulkan via torpedo tube.

U-3 began her World War I career as a training boat from 1 August 1914 to 11 November 1918.

On 1 December 1918, the surrendered boat was being towed to Preston to be broken up when she sank.