Ecosystem recovery from the end-Permian mass extinction took around 5 million years of the Early Triassic. In the pelagic deep-sea of the superocean Panthalassa, deposition of bedded chert ceased during this period, and instead, siliceous claystone lithofacies with minor chert beds was deposited. The reappearance of bedded chert around the Early-Middle Triassic (Olenekian-Anisian) boundary (OAB) was assumed to be related to recovery of radiolarian production in the pelagic realm. This study reports a new pelagic deep-sea section covering the transition from siliceous claystone lithofacies to bedded chert from Ogama in Tochigi Prefecture, Japan. Based on conodont and radiolarian biostratigraphy and carbon isotope stratigraphy, the Ogama section was dated as uppermost Olenekian to middle Anisian. The OAB was recognised by the occurrence of the conodont Chiosella timorensis, while the radiolarian-based OAB adopted by previous studies on bedded chert in Japan was revealed to be within the middle Anisian. In the Ogama section, the transition from siliceous claystone lithofacies to bedded chert is in the middle Anisian. The OAB is characterised by black organic-rich siliceous claystone, which implies oceanic oxygen depletion. Importantly, the linear sedimentation rate of the siliceous claystone lithofacies was found to be higher than that of Middle Triassic and Jurassic bedded chert. This shows that increased accumulation of clastic material was an important factor that caused the deposition of siliceous claystone in the pelagic Panthalassa at the OAB. Hence, the deposition of black siliceous claystone at the OAB may have occurred under different conditions from that at the end-Permian mass extinction, which is thought to be a result of diminished biogenic silica production.