To treat autoimmune diseases, it is important to identify which peptides bind to major histocompatibility complex (MHC) class II molecules (HLA-DRs). Predicting the peptides that bind to MHC class II molecules can effectively reduce the number of experiments required for identifying helper T cell epitopes. In our previous study, we applied fuzzy neural networks (FNNs) to solve this problem. However, an FNN requires a long calculation time and a large number of peptides; this means performing several experiments. In this study, we applied a boosted fuzzy classifier with the SWEEP operator method (BFCS) to solve this problem. For comparison, two other conventional modeling methods, namely, support vector machine and FNN combined with the SWEEP operator method (FNN-SWEEP) instead of using solely an FNN, were employed. Compared with FNN, FNN-SWEEP is extremely fast and has an almost identical prediction accuracy. The model constructed by BFCS showed an accuracy approximately 5%-10% higher than that constructed by FNN-SWEEP. In addition, BFCS was 30,000-120,000 times faster than FNN-SWEEP. This result suggests that BFCS has the potential to function as a new method of predicting peptides that bind to various protein receptors.