A rod seal assembly for a Stirling Engine of the type having two or more piston assemblies reciprocating within cylinder bores. The rod seal assembly seals against a connecting rod extending between a piston and a kinematic drive system. The rod seal assembly includes a separated cap seal assembly and a base seal assembly with a hollow cavity formed therebetween. The cap seal assembly and base seal assembly include sealing element features which provide high performance gas sealing and excellent durability characteristics. The hollow interior cavity of the rod seal assembly may be used as part of an internal volume within the engine used as part of a pressure balancing system for the isolated cycle volumes within the engine.