[4] The source of the Namyndykan is in the northern end of the Kongin Range of the Kolyma Mountains, by the southern limit of the Yukaghir Highlands.

The river heads across an uninhabited area and flows roughly eastwards until its mouth.

In its last stretch the Namyndykan reaches the Omolon floodplain where it bends northeastwards before the confluence.

[3][4] The Namyndykan joins the left bank of the Omolon in the area where the great river makes a bend northwards.

The confluence is 466 kilometres (290 mi) from the mouth of the Omolon, near the border of the Chukotka Autonomous Okrug.