Agrophotovoltaic (APV) system is an integrated system producing crops as well as solar energy. Because crop production underneath Photovoltaic (PV) modules requires delicate management of crops, smart farming equipment such as real-time remote monitoring sensors (e.g., soil moisture sensors) and micro-climate monitoring sensors (e.g., thermometers and irradiance sensors) is installed in the APV system. This study aims at introducing a decision support system (DSS) for smart farming in an APV system. The proposed DSS is devised to provide a mobile application service, satellite image processing, real-time data monitoring, and performance estimation. Particularly, the real-time monitoring data is used as an input of the DSS system for performance estimation of an APV system in terms of production yields of crops and monetary benefit so that a data-driven function is implemented in the proposed system. The proposed DSS is validated with field data collected from an actual APV system at the Jeollanamdo Agricultural Research and Extension Services in South Korea. As a result, farmers and engineers enable to efficiently produce solar energy without causing harmful impact on regular crop production underneath PV modules. In addition, the proposed system will contribute to enhancement of the smart farming technology in the field of agriculture.