Structural health monitoring (SHM) is essential for composite unmanned aerial vehicles (UAVs). Additionally, because UAVs are extremely sensitive to weight and volume, the minimal addition of weight and volume by the SHM system is crucial. Therefore, we proposed a compact and lightweight wireless SHM sensor node and an embedded carbon nanotube (CNT) fiber sensor for in-flight SHM of UAVs. The wireless SHM sensor node was composed of an analog sensing circuit, wireless microcontroller unit, and analog low pass filter. The small diameter CNT fiber sensor was developed to be easily embedded inside composite structures and to enhance their structural properties while performing as an SHM sensor. Glass composite skin with embedded CNT fiber sensors composed of ultra-high-molecular-weight polyethylene, polyurethane, CNT, and carbon black were installed in the aircraft. For comparison, a strain gauge attached at the center of a long CNT fiber sensor was also used during in-flight measurement. In-flight strain measurements from both the CNT fiber sensor and the strain gauge were continuously transmitted to the ground station and were compared with the flight data. Furthermore, an impact tester was installed inside the wing to simulate impact during flight, and in-flight impact measurements by the CNT fiber sensor were demonstrated.