The thermoelectric effect is attracting a renewed interest as a concept for energy harvesting technologies. Nanomaterials have been considered a key to realize efficient thermoelectric conversions owing to the low dimensional charge and phonon transports. In this regard, recently emerging two-dimensional materials could be promising candidates with novel thermoelectric functionalities. Here we report that FeSe ultrathin films, a high-Tc superconductor (Tc; superconducting transition temperature), exhibit superior thermoelectric responses. With decreasing thickness d, the electrical conductivity increases accompanying the emergence of high-Tc superconductivity; unexpectedly, the Seebeck coefficient α shows a concomitant increase as a result of the appearance of two-dimensional natures. When d is reduced down to ~1 nm, the thermoelectric power factor at 50 K and room temperature reach unprecedented values as high as 13,000 and 260 μW cm-1 K-2, respectively. The large thermoelectric effect in high Tc superconductors indicates the high potential of two-dimensional layered materials towards multi-functionalization.