Scientists believe that the submarine came into contact with a mine which came into ignition somewhere at the top of the vessel.
"It's quite wonderful that we found something like this", Western Flanders Gov. Carl Decaluew said.
However, one unconfirmed report in the Belgian media has stated the wreck is close to the port of Ostende.
As many as 23 bodies could be on board the sub, which is lying on its starboard side on the seabed.
"This sort of submarine would have had a standard crew of 22 and one commander", said Mr Decaluwé.
It is not clear which of the known 11 wrecks of German submarines has been found, but "Of the 11 downed U-boats in Belgian waters, this one is the best preserved example", the province said, Reuters reported.
Although in good condition, there is still damage to the whole wreckage, especially at the bow.
The conning tower is described as intact and the periscopes are still visible.
Two torpedo tubes were found destroyed a the site of the wreck. According to researchers the submarine may have become caught up in the cable of the mine, dragging it up towards the surface and leading to it doing the damage, putting the submarine out of action.
UB-II submarines were built in 1915 and 1916 and were able to dive to a depth of around 50m.
The find, which came after underwater scans suggested there could be a wreck in Belgian waters, was confirmed today by the governor of West Flanders.