This study aimed to develop and evaluate a deep learning-based system for the automatic measurement of angles (specifically, Meary’s angle and calcaneal pitch) in weight-bearing lateral radiographs of the foot for flatfoot diagnosis. We utilized 3960 lateral radiographs, either from the left or right foot, sourced from a pool of 4000 patients to construct and evaluate a deep learning-based model. These radiographs were captured between June and November 2021, and patients who had undergone total ankle replacement surgery or ankle arthrodesis surgery were excluded. Various methods, including correlation analysis, Bland–Altman plots, and paired T-tests, were employed to assess the concordance between the angles automatically measured using the system and those assessed by clinical experts. The evaluation dataset comprised 150 weight-bearing radiographs from 150 patients. In all test cases, the angles automatically computed using the deep learning-based system were in good agreement with the reference standards (Meary’s angle: Pearson correlation coefficient (PCC) = 0.964, intraclass correlation coefficient (ICC) = 0.963, concordance correlation coefficient (CCC) = 0.963, p-value = 0.632, mean absolute error (MAE) = 1.59°; calcaneal pitch: PCC = 0.988, ICC = 0.987, CCC = 0.987, p-value = 0.055, MAE = 0.63°). The average time required for angle measurement using only the CPU to execute the deep learning-based system was 11 ± 1 s. The deep learning-based automatic angle measurement system, a tool for diagnosing flatfoot, demonstrated comparable accuracy and reliability with the results obtained by medical professionals for patients without internal fixation devices.