Abstract In recent years, unmanned aerial vehicle (UAV) autonomous flight technology has been applied in many fields. However, in the process of autonomous operation, the UAV may deviate from the set flight path due to various disturbance factors, which results in mission failure. In order to find the abnormal situation in time and take corresponding measures, it is necessary to monitor the operation state of the UAV. Predicting the UAV flight path is the main monitoring method at present; however, the accuracy and real-time of the existing prediction methods are limited. Therefore, this paper proposes an error compensation Bessel bidirectional long short-term memory real-time path prediction model deployed in ground stations. First, because of inconsistency of the units in all directions of the original positioning information provided by global positioning system, the Bessel geodetic coordinate transformation is introduced to unify the units of three-dimensional coordinate data, so as to improve the prediction accuracy. Second, considering the problems of poor data quality and data missing in the operation process, the least square fitting method is used to supplement and correct the positioning coordinate data to obtain more reliable and accurate path observation values as the model input. Finally, a deep learning path prediction model based on bi-directional long short-term memory (BiLSTM) network is constructed, and the appropriate network parameters are determined with the prediction accuracy and time as evaluation indicators. In order to further improve the prediction accuracy, a compensator based on proportional integral differential error control theory is designed according to the output characteristics of the BiLSTM network, which is used for providing compensation values for the prediction results of the model. The training and testing results using the actual flight data of UAV operation show that, under the experimental environment built, the model proposed in this paper can complete the UAV flight path prediction with root mean square error < 1 meter within 0.1 second, and has better performance and higher prediction accuracy than other neural network models.