Conglomerates, exposed on either side of the Yarlung Tsangpo suture zone (YTSZ) in southern Tibet, have attracted wide attention in elucidating uplift and erosion histories of the Himalayan-Tibetan orogen. However, the provenance of these conglomerates remains controversial. Although radiolarian-bearing chert clasts within these conglomerates have received little focus, identification of the radiolarian assemblages they contain could shed light on the provenance of these sedimentary units. We present the first report of Upper Jurassic to Lower Cretaceous (upper Kimmeridgian–lower Barremian) radiolarian assemblages recovered from chert clasts within the Liuqu and Gangrinboche conglomerates in the Xigaze area. To extract radiolarian fossils from independent clasts in the conglomerates, a detailed and efficient experimental process is illustrated. The assemblages are well correlated to those in the YTSZ and Tethyan Himalaya, showing typical Tethyan characteristics. The lithology of chert clasts and ages of constituent radiolarian faunas suggest that the chert clasts in Liuqu and Gangrinboche conglomerates were derived from the Bainang terrane. This interpretation implies that Early Cretaceous accretionary complexes in the YTSZ had been exposed and eroded before deposited as clasts in the Cenozoic Liuqu and Gangrinboche conglomerates.