We report about Self-Potential (SP) anomalies registered 150 m from the active lava dome of Merapi Volcano, which are associated with Ultra-Long-Period (ULP) seismic signals (periods >100 s). During a 5-month period of simultaneous SP and seismological measurements, 50 ULP events were detected seismologically. If SP time series corresponding to ULP events are aligned to the onset times of ULP-events and stacked, the resulting traces show anomalous SP with an amplitude of 5--20 mV/km and 40--60 min duration. In contrast, the anomalous signals were not present in ground temperature data nor in SP data recorded ≈1 km from the summit. SP anomalies associated with ULP-seismicity might be caused by electro-kinetic effect of fluid flow in subsurface. This result is consistent with the ULP-generation model based on seismological observations and adds new information towards the understanding of ULP-seismicity.