Localization of unmanned aircraft systems (UASs) in indoor scenarios and GNSS-denied environments is a difficult problem, particularly in dynamic scenarios where traditional on-board equipment (such as LiDAR, radar, sonar, camera) may fail. In the framework of autonomous UAS missions, precise feedback on real-time aircraft position is very important, and several technologies alternative to GNSS-based approaches for UAS positioning in indoor navigation have been recently explored. In this paper, we propose a low-cost IPS for UAVs, based on Bluetooth low energy (BLE) beacons, which exploits the RSSI (received signal strength indicator) for distance estimation and positioning. Distance information from measured RSSI values can be degraded by multipath, reflection, and fading that cause unpredictable variability of the RSSI and may lead to poor-quality measurements. To enhance the accuracy of the position estimation, this work applies a differential distance correction (DDC) technique, similar to differential GNSS (DGNSS) and real-time kinematic (RTK) positioning. The method uses differential information from a reference station positioned at known coordinates to correct the position of the rover station. A mathematical model was established to analyze the relation between the RSSI and the distance from Bluetooth devices (Eddystone BLE beacons) placed in the indoor operation field. The master reference station was a Raspberry Pi 4 model B, and the rover (unknown target) was an Arduino Nano 33 BLE microcontroller, which was mounted on-board a UAV. Position estimation was achieved by trilateration, and the extended Kalman filter (EKF) was applied, considering the nonlinear propriety of beacon signals to correct data from noise, drift, and bias errors. Experimental results and system performance analysis show the feasibility of this methodology, as well as the reduction of position uncertainty obtained by the DCC technique.