Detrital zircon geochronology has rapidly evolved into a powerful tool for reconstructing the assembly and dispersal processes of supercontinents. Currently, the dispersal history of Gondwanaland remains highly controversial. Here we focus on detrital zircon geochronology of the Gondwana (Carboniferous–Permian Kokaha Diamictite and Jurassic–Cretaceous Sapt Koshi Formation) and post-Gondwana (Miocene Tamrang Formation) sequences of the Lesser Himalaya in eastern Nepal. Detrital zircon U-Pb dating results show that the Carboniferous–Permian sequence peaks at 544 Ma, 890 Ma, 1178 Ma, and 1752 Ma. Likewise, the Jurassic–Cretaceous sequence peaks at 531 Ma, 947 Ma, 1176 Ma and 1806 Ma along with a much younger peak at 123 Ma. Similarly, the Miocene sequence peaks at 526 Ma, 987 Ma, and 1740 Ma. Comparing these newly obtained ages with those of surrounding regions, we confirm that during the Carboniferous–Permian, the Indian continent was still connected to Gondwana. The U-Pb age distribution of the Kokaha Diamictite coincides with that of the Tethys Himalaya, which further suggests the possibility that this unit either shared the same provenance with or was recycled from the Tethys Himalaya. During the early Mesozoic, the Indian plate rifted from Gondwana and drifted northward, as evidenced by Triassic–Jurassic, rift-related magmatism along the Indian continental margin. Remarkably, there were significant inputs from the Rajmahal Basalt during deposition of the Jurassic–Cretaceous sequence. Besides, the Miocene sequence records a large number of zircons that closely resemble those of the Greater Himalaya, which implies that the Greater Himalaya may have already been uplifted and eroded by then.