This research presents an in-depth examination of the emotional effects of synchronous hybrid education on undergraduate university students at a pioneering private institution in educational innovation. The study had encompassed all courses that were delivered in a synchronous hybrid format, covering 16 courses and involving 241 students. Each student had been observed and recorded on two separate class sessions, with each recording lasting approximately 30 min. This comprehensive data collection had resulted in 409 recordings, each approximately 30 min in duration, translating to nearly an hour of observation per student across the classes, totaling close to 205 h of recordings. These recordings were subsequently processed using neuroscience software tools for advanced statistical analysis, effectively serving as a comprehensive survey of courses within this modality. The primary focus of the research was on the emotions experienced during both face-to-face and online classes and their subsequent influence on student behavior and well-being. The findings reveal higher emotional time ratios for positive emotions such as joy and surprise in face-to-face students. Notably, both groups exhibited comparable ratios for negative emotions like anger and sadness. The research underscores the emotional advantages of face-to-face interactions, which elicit stronger emotions, in contrast to online students who often feel detached and isolated.