Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is a neurological disease that occurs as a result of damage to the nerves in the brain and restriction of muscle movements. Electroencephalography (EEG) is the most common method used in brain imaging to study neurological disorders. Diagnosis of neurological disorders such as ALS, Parkinson’s, attention deficit hyperactivity disorder is important in biomedical studies. In recent years, deep learning (DL) models have been started to be applied in the literature for the diagnosis of these diseases. In this study, event-related potentials (ERPs) were obtained from EEG signals obtained as a result of visual stimuli from ALS patients and healthy controls. As a new method, variational mode decomposition (VMD) is applied to the produced ERP signals and the signals are decomposed into subbands. In addition, empirical mode decomposition (EMD), one of the popular decomposition methods in the literature, was also analyzed, and ERP signals were divided into subbands and compared with the VMD method. Subband signals were classified in two stages with the one-dimensional convolutional neural network (1D CNN) model, which is one of the DL techniques proposed in the study. Accuracy, sensitivity, specificity, and F1-Score measurements were obtained using 5- and 10-fold cross-validation to evaluate classifier performance. In the first stage of classification, only VMD and EMD subband signals were used and 92.95% classification accuracy was obtained by the VMD method. In the second stage, VMD, EMD subband signals, and original ERP signals were all classified together with the VMD+ERP model achieving the maximum classification accuracy rate of 90.42%. It is thought that the results of the study will contribute to the diagnosis of similar neurological disorders such as ALS, attention studies based on visual stimuli, and the development of brain-computer interface (BCI) systems using the method applied to the proposed ERP signals.