The Kukhtuy river has its source at an elevation of 1,617 m (5,305 ft) in the Suntar-Khayata range.
It flows relatively straight southwards through a mountainous area. The Yudoma Range rises on the right side and the Kukhtuy Range on the left side of its valley and its course is roughly parallel to rivers Okhota to the west and Ulbeya to the east.[1][3]
South of the 61st parallel the river valley widens and the Kukhtuy meanders across a widening floodplain with many bogs and small lakes. Finally it flows into the Sea of Okhotsk on the northeastern side of the estuary of Okhotsk town.[4]
The main tributary of the Kukhtuy is the 178 kilometres (111 mi) long Gusinka (Гусинка) that joins it from the left. The river freezes around late October and stays frozen until mid May.