Addressing the difficult problem of predicting the height of water-conducting fracture zones in shallow and thin coal seams, a prediction model of water-conduction fracture zones based on a backpropagation (BP) neural network was developed by integrating theoretical analysis, field measurements, and algorithmic advancements. Firstly, through overburden migration analysis and correlation tests, the height index system of the water-conducting fracture zone was determined. This system includes mining height, buried depth, dip angle, working face width, and overburden rock lithology, with five groups of characteristic parameters. Then, 35 pairs of minefield-measured data were collected to establish the measured height data set of the water-conducting fracture zone. Secondly, a BP neural network prediction model and a traditional support vector regression (SVR) prediction model were constructed based on a Pytorch framework, and the models were trained and tested by selecting data sets. Thirdly, the optimal prediction model was determined by comparing the model with the empirical model and multiple regression model of mining regulations for coal pillar maintenance and pressure in buildings, water bodies, railways, and main shafts. Finally, a typical mine was selected for application to verify the suitability of the optimal model. The results show that: (1) the predicted value of the neural network model is consistent with the change trend of the measured value, which accords with the theoretical law; (2) compared with traditional forecasting methods, the error of the BP neural network prediction model is stable and the prediction effect is the best; (3) dropout can effectively mitigate mitigation training overfitting, achieve regularization, and improve prediction accuracy; (4) the field application further verified that the BP neural network model is the best for predicting the height of water-conducting fracture zones of extremely thin coal seams, and the research results can provide technical guidance for similar fragile coal seams.