The purpose of this study is to identify the educational effects of scientific observation learning programs based on universal design for learning (UDL) from a cognitive thought process perspective through EEG activation analysis. To this end, we developed EEG measurement tasks and scientific observation learning programs based on the UDL. The study involved 14 high school students. EEG data collection took place while students performed scientific observation tasks before and after their experience with scientific observation learning programs based on the UDL. Comparative analysis of pre & post EEG data was performed using the sLORETA analysis method. The results of the study are as follows. First, The experimental group students scored higher on the scientific observation knowledge generation in the post-task than the control group students. And the scientific observation knowledge generation scores of the students in the experimental group were further improved than control group student. Second, in the case of the theta band, activation was significantly decreased in cuneus, middle occipital gyrus, lingual gyrus, and angular gyrus during performing the post-tasks compared to performing the pre-tasks. For the alpha band, activation was significantly decreased in superior frontal gyrus, middle frontal gyrus, inferior frontal gyrus, and superior temporal gyrus during performing the post-tasks. On the other hand, the alpha band activation was increased in precuneus and angular gyrus during post-task performance. For the beta band, activation was decreased during preforming the post-tasks compared to performing the pre-tasks in superior parietal lobule, inferior parietal lobule, precuneus, angular gyrus, and postcentral gyrus. Finally, for the gamma band, when performing the post-tasks compared to performing the pre-tasks, activation was decreased in superior parietal lobule, inferior parietal lobule, precuneus, angular gyrus, postcentral gyrus, and cingulate gyrus. This result shows that scientific observation learning programs based UDL have a positive impact on cognitive thinking process performed by students performed to identify the entire and partial elements of an observation object. This cognitive thinking process included recognition of visual information, retrieval and review of long-term memory, and ascription of meaning to collected visual information, and working memory about visual information.