Various studies have measured and analyzed learners’ emotions in both traditional classroom and e-learning settings. Learners’ emotions can be estimated using their text input, speech, body language, or facial expressions. The presence of certain facial expressions has shown to indicate a learner’s levels of concentration in both traditional and e-learning environments. Many studies have focused on the use of facial expressions in estimating the emotions experienced by learners. However, little research has been conducted on the use of analyzed emotions in estimating the learning affect experienced. Previous studies have shown that online learning can enhance students’ motivation, interest, attention, and performance as well as counteract negative emotions, such as boredom and anxiety, that students may experience. Thus, it is crucial to integrate modules into an existing e-learning platform to effectively estimate learners’ learning affect (LLA), provide appropriate feedback to both learner and lecturers, and potentially change the overall online learning experience. This paper proposes a learning affect estimation framework that employs relational reasoning for facial expression recognition and adaptive mapping between recognized emotions and learning affect. Relational reasoning and deep learning, when used for autoanalysis of facial expressions, have shown promising results. The proposed methodology includes estimating a learner’s facial expressions using relational reasoning; mapping the estimated expressions to the learner’s learning affect using the adaptive LLA transfer model; and analyzing the effectiveness of LLA within an online learning environment. The proposed research thus contributes to the field of facial expression recognition enhancing online learning experience and adaptive learning.