The submarine was powered by two six-cylinder four-stroke diesel engines each producing 300 metric horsepower (220 kW; 300 shp) (a total of 600 metric horsepower (440 kW; 590 shp)), two electric motors producing 770 metric horsepower (570 kW; 760 shp), and two propeller shafts.

She had a dive time of 15 seconds and was capable of operating at a depth of 75 metres (246 ft).

When submerged, she could operate for 40 nautical miles (74 km; 46 mi) at 4.5 knots (8.3 km/h; 5.2 mph); when surfaced, she could travel 9,850 nautical miles (18,240 km; 11,340 mi) at 7 knots (13 km/h; 8.1 mph).

UC-99 was fitted with six 100 centimetres (39 in) mine tubes, fourteen UC 200 mines, three 50 centimetres (20 in) torpedo tubes (one on the stern and two on the bow), seven torpedoes, and one 10.5 cm (4.1 in) SK L/45 or 8.8 cm (3.5 in) Uk L/30 deck gun .

[Note 1] As with the rest of the completed UC III boats, UC-99 conducted no war patrols and sank no ships.