To improve designs of e-learning materials, it is necessary to know which word or figure a learner felt "difficult" in the materials. In this pilot study, we measured electroencephalography (EEG) and eye gaze data of learners and analyzed to estimate which area they had difficulty to learn. The developed system realized simultaneous measurements of physiological data and subjective evaluations during learning. Using this system, we observed specific EEG activity in difficult pages. Integrating of eye gaze and EEG measurements raised a possibility to determine where a learner felt “difficult” in a page of learning materials. From these results, we could suggest that the multimodal measurements of EEG and eye gaze would lead to effective improvement of learning materials. For future study, more data collection using various materials and learners with different backgrounds is necessary. This study could lead to establishing a method to improve e-learning materials based on learners' mental states.