The effect of initial electrolyte loading (IEL) on cell performance in a coin-type molten carbonate fuel cell (MCFC) was investigated in this work. Since the material of MCFC depends on the manufacturer, optimisation requires experimental investigation. In total, four IEL values, 1.5, 2.0, 3.0, and 4.0 g, were used, corresponding to a pore filling ratio (PFR) of 38, 51, 77, and 102%, respectively. The cell performance with respect to the PFR was analysed via steady-state polarisation, step-chronopotentiomtery, and impedance methods. The electrochemical analyses revealed that internal resistance and overpotential of the cell decreased with increasing PFR, and a large overpotential was observed when the PFR was 102%, probably due to the flooding phenomenon. After operation, cross-section of the cell was analysed via surface analysis of SEM and EDS methods, and the remaining electrolyte was estimated by dissolution of the cell in 10 wt% acetic acid. A linear relationship between IEL and the weight reduction ratio by dissolution was obtained. Thus, the remaining amount of electrolyte could be measured after operation. The results of SEM and EDS showed that a PFR of 38 and 102% showed a lack and flooding of electrolytes at the cell, respectively, which led to a large overpotential. This work reports that MCFC performance is allowed only in the narrow range of PFR.