German submarine U-3039 was a Type XXI U-boat (one of the "Elektroboote") of Nazi Germany's Kriegsmarine, built for service in World War II. She was ordered on 6 November 1943, and was laid down on 29 November 1944 at AG Weser, Bremen, as yard number 1198. She was launched on 14 February 1945, and commissioned under the command of Kapitänleutnant Günther Ruperti on 8 March 1945.
Like all Type XXI U-boats, U-3039 had a displacement of when at the surface and while submerged. She had a total length of (o/a), a beam of , and a draught of . The submarine was powered by two MAN SE supercharged six-cylinder M6V40/46KBB diesel engines each providing , two Siemens-Schuckert GU365/30 double-acting electric motors each providing , and two Siemens-Schuckert silent running GV232/28 electric motors each providing .
The submarine had a maximum surface speed of and a submerged speed of . When running on silent motors the boat could operate at a speed of . When submerged, the boat could operate at for ; when surfaced, she could travel at . U-3039 was fitted with six torpedo tubes in the bow and four C/30 anti-aircraft guns. She could carry twenty-three torpedoes or seventeen torpedoes and twelve mines. The complement was five officers and fifty-two men.
U-3039 was scuttled on 3 May 1945, at Kiel, as part of Operation Regenbogen. The wreck was later raised and broken up.