Abnormal foot postures may affect foot movement and joint loading during locomotion. Investigating foot posture alternation during running could contribute to injury prevention and foot mechanism study. This study aimed to develop feature-based and deep learning algorithms to predict foot pronation during prolonged running. Thirty-two recreational runners have been recruited for this study. Nine-axial inertial sensors were attached to the right dorsum of the foot and the vertical axis of the distal anteromedial tibia. This study employed feature-based machine learning algorithms, including support vector machine (SVM), extreme gradient boosting (XGBoost), random forest, and deep learning, i.e., one-dimensional convolutional neural networks (CNN1D), to predict foot pronation. A custom nested k-fold cross-validation was designed for hyper-parameter tuning and validating the model’s performance. The XGBoot classifier achieved the best accuracy using acceleration and angular velocity data from the foot dorsum as input. Accuracy and the area under curve (AUC) were 74.7 ± 5.2% and 0.82 ± 0.07 for the subject-independent model and 98 ± 0.4% and 0.99 ± 0 for the record-wise method. The test accuracy of the CNN1D model with sensor data at the foot dorsum was 74 ± 3.8% for the subject-wise approach with an AUC of 0.8 ± 0.05. This study found that these algorithms, specifically for the CNN1D and XGBoost model with inertial sensor data collected from the foot dorsum, could be implemented into wearable devices, such as a smartwatch, for monitoring a runner’s foot pronation during long-distance running. It has the potential for running shoe matching and reducing or preventing foot posture-induced injuries.