The origins and age distribution of the Himalayan high-pressure (HP) and ultrahigh-pressure (UHP) metamorphic rocks are critical for understanding the pre-Himalayan history. Although the protoliths to the UHP Tso Morari eclogites in Ladakh, NW Himalaya are believed to be the Permian Panjal volcanics, the geochronological evidence is absent. Here, we demonstrate that the protoliths of the UHP Tso Morari Complex formed in a continental rift setting at the Indian margin associated with the northern East Gondwana during the Early Paleozoic. Zircon U–Pb dates from eight gneisses and one garnet amphibolite indicate the Early Paleozoic bimodal magmatism of 493–476 Ma, which could be associated with the separation of South China from North India. Except for arc-related eclogites found in the Nidar ophiolite, the eclogites and amphibolites are rift-related, exhibiting enriched light rare earth elements and high concentrations of incompatible elements, along with evidence for crustal contamination. Our findings support the previously reported diversity in the sources and ages of the protoliths of the Himalayan HP–UHP metamorphic rocks along the orogen.