A residential ground-source heat pump system often requires a long payback time to recover the capital cost. Long-term uncertainty in such a system’s performance increases as the climate changes. This study compares 20-years hourly heating/cooling demands of a typical residence in the present (2000–2020) and in the future (2076–2095) for two locations in Japan. This study also calculated soil temperatures as heat sources through 1D heat-transfer simulation based on the A1B climate scenario in the Intergovernmental Panel on Climate Change’s Special Report. System performance and simple payback times were compared in one cold and one warm city in Japan (Sapporo and Tokyo, respectively). Soil temperatures at a middle depth of a borehole heat exchanger were predicted to increase in the future by ~1 °C, with insignificant effects on a borehole heat exchanger. Seasonal performance factors increased in Sapporo because thermal demands would be kept even in the future, but decreased in Tokyo, which has a higher ratio of the energy used in operating the system in cooling mode compared with its small heating demand. The simple payback time was estimated at 16.2 and >20 years in Sapporo and Tokyo, respectively, both in the present and future, with the constant energy prices. If oil and gas prices doubled, the payback time would be halved in Sapporo to 8.4 years but remain around 20 years or more in Tokyo.