Emotions are very important during learning and assessment procedures. However, measuring emotions is a very demanding task. Several tools have been developed and used for this purpose. In this paper, the efficiency of the FaceReader during a computer-based assessment (CBA) was evaluated. Instant measurements of the FaceReader were compared with the researchers’ estimations regarding students’ emotions. The observations took place in a properly designed room in real time. Statistical analysis showed that there are some differences between FaceReader’s and researchers’ estimations regarding Disgusted and Angry emotions. Results showed that FaceReader is capable of measuring emotions with an efficacy of over 87% during a CBA and that it could be successfully integrated into a computer-aided learning system for the purpose of emotion recognition. Moreover, this study provides useful results for the emotional states of students during CBA and learning procedures. This is actually the first time that student’s instant emotions were measured during a CBA, based on their facial expressions. Results showed that most of the time students were experiencing Neutral, Angry, and Sad emotions. Furthermore, gender analysis highlights differences between genders’ instant emotions.