This study investigated the neural dynamics associated with short-term exposure to different virtual classroom designs with different window placement and room dimension. Participants engaged in five brief cognitive tasks in each design condition including the Stroop Test, the Digit Span Test, the Benton Test, a Visual Memory Test, and an Arithmetic Test. Performance on the cognitive tests and Electroencephalogram (EEG) data were analyzed by contrasting various classroom design conditions. The cognitive-test-performance results showed no significant differences related to the architectural design features studied. We computed frequency band-power and connectivity EEG features to identify neural patterns associated to environmental conditions. A leave one out machine learning classification scheme was implemented to assess the robustness of the EEG features, with the classification accuracy evaluation of the trained model repeatedly performed against an unseen participant's data. The classification results located consistent differences in the EEG features across participants in the different classroom design conditions, with a predictive power that was significantly higher compared to a baseline classification learning outcome using scrambled data. These findings were most robust during the Visual Memory Test, and were not found during the Stroop Test and the Arithmetic Test. The most discriminative EEG features were observed in bilateral occipital, parietal, and frontal regions in the theta and alpha frequency bands. While the implications of these findings for student learning are yet to be determined, this study provides rigorous evidence that brain activity features during cognitive tasks are affected by the design elements of window placement and room dimensions.