The settlement was founded in connection with the beginning of the construction of the road from the river Aldan to Oymyakon the main designer of this road, the head of Dalstroi NKVD Mikhail Konstantinovich Karpov. When the question of building a highway was discussed in the 1930s, the village of Krest-Khaldjay was designated as the initial picket of the future road, but Karpov decided to build it from a new point in order to reduce the road and therefore chose the shore of Aldan, which was 80 km higher than the village of Krest-Khaldjay . Near the village to this day, a symbolic sign of the beginning of the Kolyma route, the so-called zero kilometer, has been preserved.

In 1957, after the camps were closed, Khandyga turned into a normal working village, not connected with punitive structures. Today in Khandyga itself almost nothing reminds of Gulag history, however, along the route of Khandyga - Topolinoe there are still abandoned buildings erected by the prisoners' hands: houses, kitchens, bridges ... In the backwoods where the human foot has not walked since the 1950s , you can find an abandoned camp in the mines.

In the village there is a river port, however, there is no regular passenger traffic with Yakutsk along the river today, although it was formerly used by hydrofoil ships. In the vicinity of the village there are many mountain rivers suitable for rafting, for example, East Khandyga.