A method for directly recovering precious metals from polymer electrolyte fuel cells (PEFCs) by electrochemical dissolution without dismantling the cells was developed. After filling a single PEFC containing Pt and Ru catalysts with 1 mol l−1 HCl solution, 100 wt% of Pt and 96 wt% of Ru dissolved into the solution by periodically changing the electric polarity of the fuel and air electrodes containing Pt and Ru metal. To confirm the adaptability of this method to cell stack assemblies (CSAs), electrochemical dissolution tests using 3- and 5-cell CSAs, and a 700 W CSA were also conducted. In the 3- and 5-cell CSA tests, 100 wt% of Pt and 95 wt% of Ru were recovered as ions. In the case of the 700 W CSA, 86.8 wt% of Pt and 88.4 wt% of Ru were recovered as ions in 9.2 L of 1 mol l−1 HCl after 180 min of electrolysis. Power consumption rates for Pt and Ru dissolution in the 700 W CSA cell were approximately 0.13 kW h g−1. Thus, the feasibility of the electrochemical dissolution method of Pt and Ru from PEFCs without dismantling PEFCs was confirmed.