Small free-flying robots to assist astronauts and perform experiments need a propulsion system to move freely in microgravity. Hardware-in-the-loop (HIL) simulators can simultaneously verify guidance, navigation, and control (GNC) systems, including flight hardware and software, in three dimensions. However, it is difficult to incorporate a small free-flying robot into the HIL simulator because of the low propulsive force and gravity compensation associated with its attitude changes. This paper proposes a HIL simulator with a propulsion subsystem mounted on a statically fixed force/torque sensor and a GNC subsystem mounted on a dynamically movable robotic arm. This simulator allows us to verify the GNC algorithms comprehensively using actual navigation sensors and propulsive actuators in an emulated flight environment. The actual capabilities of this simulator were successfully demonstrated in motion verifications of a free-flying robot, the Int-Ball2.