The clearance flow channel (CFC) of pump-turbine is a thin cavity composed of a runner and head cover or bottom ring, but excessive pressure pulsation in a flat CFC is easy to cause the head cover excitation. At present, there are insufficient studies on the flow patterns, and pressure pulsations in CFC. In this paper, the 3D CFD numerical simulation method was used to reveal the flow patterns, and pressure pulsations in the CFC of a low specific speed pump-turbine under rotational stall condition. The results showed that the stall vortexes rotated in the vaneless region of the main flow channel (MFC) when the rotating stall occurred in the pump mode; while that rotated in the runner flow channels, causing circumferentially imbalanced pressure at the runner inlet, as well as a low-frequency and high-amplitude pulsation in MFC. In CFC, uneven pressure distribution in the external cavity was formed when the clearance inlet pressure was unbalanced in the circumferential direction in turbine braking mode. The pulsation generated by the rotating stall in the MFC could be transmitted to the CFC, but the pulsation amplitude dropped sharply at the clearance inlet position, then increased first and ultimately decreased inward along the clearance flow channel. This study provides a reference for the study of hydraulic excitation of the head cover.