Electromyography is a valuable diagnostic procedure for diagnosing patients with neuromuscular diseases; however, it has some drawbacks. First, diagnosis using electromyography is subjective, and in some cases, there is the potential for inter-individual discrepancies. Second, it is a time- and effort-intensive process that requires expertise to yield accurate results. Recently, a deep learning algorithm shows effectiveness for the analysis of waveform data such as electrocardiography. To overcome limitations of electromyography, we developed a deep learning-based electromyography classification system and compared the performance of our deep learning model with that of six physicians. This study included 58 subjects who underwent electromyography and were finally confirmed as having myopathy or neuropathy, or to be in a normal state between June 2015 and July 2020 at Seoul National University Hospital. We developed a one-dimensional convolutional neural network algorithm and divide-and-vote system for diagnosing subjects. Diagnosis results with our deep learning model were compared with those of six physicians with experience in performing and interpreting electromyography. The accuracy, sensitivity, specificity, and positive predictive value of the deep learning model for diagnosis as to whether subjects have myopathy or neuropathy or normal were 0.875, 0.820, 0.904, and 0.820, respectively, whereas those for the physicians were 0.694, 0.537, 0.773, and 0.524, respectively. The area under the receiver operating characteristic curves of the deep learning model for predicting myopathy, neuropathy, and normal states was better than the averaged results of six physicians. Our study showed that deep learning could play a key role in reading electromyography and diagnosing patients with neuromuscular diseases. In the future, large prospective cohort studies incorporating diverse neuromuscular diseases can enable deep learning-based electrodiagnosis on behalf of physicians.