Today, due to the widespread outbreak of the deadly coronavirus, popularly known as COVID-19, the traditional classroom education has been shifted to computer-based learning. Students of various cognitive and psychological abilities participate in the learning process. However, most students are hesitant to provide regular and honest feedback on the comprehensiveness of the course, making it difficult for the instructor to ensure that all students are grasping the information at the same rate. The students’ understanding of the course and their emotional engagement, as indicated via facial expressions, are intertwined. This paper attempts to present a three-dimensional DenseNet self-attention neural network (DenseAttNet) used to identify and evaluate student participation in modern and traditional educational programs. With the Dataset for Affective States in E-Environments (DAiSEE), the proposed DenseAttNet model outperformed all other existing methods, achieving baseline accuracy of 63.59% for engagement classification and 54.27% for boredom classification, respectively. Besides, DenseAttNet trained on all four multi-labels, namely boredom, engagement, confusion, and frustration has registered an accuracy of 81.17%, 94.85%, 90.96%, and 95.85%, respectively. In addition, we performed a regression experiment on DAiSEE and obtained the lowest Mean Square Error (MSE) value of 0.0347. Finally, the proposed approach achieves a competitive MSE of 0.0877 when validated on the Emotion Recognition in the Wild Engagement Prediction (EmotiW-EP) dataset.