We performed U-Pb dating of detrital zircons collected from Middle–Upper Jurassic strata of the Sugoi synclinorium and Cretaceous rocks of the Omsukchan (Balygychan-Sugoi) basin, in order to identify their provenance and correlate Jurassic–Cretaceous sedimentation of the south-eastern Verkhoyansk-Kolyma orogenic belt with various Magmatic belts of the north-east Asia active Margins. In the Middle–Late Jurassic, the Uda-Murgal Magmatic arc represented the Main source area of clastics, suggesting that the Sugoi basin is a back-arc basin. A Major shift in the provenance signature occurred during the Aptian, when granitoids of the Main (Kolyma) batholith belt, along with volcanic rocks of the Uyandina-Yasachnaya and Uda-Murgal arcs, became the Main sources of clastics deposited in the Omsukchan basin. In a final Mesozoic provenance shift, granitoids of the Main (Kolyma) batholith belt, along with volcanic and plutonic rocks of the Uyandina-Yasachnaya and Okhotsk-Chukotka arcs, became the dominant sources for clastics in the Omsukchan basin in the latest Cretaceous. A broader comparison of detrital zircon age distributions in Jurassic–Cretaceous deposits across the south-eastern Verkhoyansk-Kolyma orogen illustrates that the Sugoi and Omsukchan basins did not form along the distal eastern portion of the Verkhoyansk passive Margin, but in the Late Mesozoic back-arc basins.