In its uppermost course the Tompo runs roughly northward along the northern side of the Suntar-Khayata mountains; after roughly 80 km (50 mi) it turns and follows a generally westward direction for about 200 km (120 mi) through the southern part of the Elgi Plateau.

Downstream from the mouth of the Delinya, its 2nd largest tributary, which flows from the central part of the Yana-Oymyakon Highlands, the Tompo bends SSE into a roughly 130 km (81 mi) long deep gorge, separating the Verkhoyansk Range proper to the northwest and the group of three parallel ranges formed by the Ulakhan-Bom, Sette-Daban and the Skalisty Range to the southeast.

After the mouth of the Menkule River, it emerges from the mountains and, flowing in a southwesterly direction, enters the eastern side of the Central Yakutian Plain, where its valley becomes very wide and swampy, its riverbed dividing into lazily-flowing arms as the speed of the flow decreases.

Finally the Tompo meets the right bank of the Aldan River, opposite Megino-Aldan village, upstream of the mouth of the Baray.

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