Predicting students’ performance in a course is one of the major aims of educational data mining systems. In the present study, two and three-layer artificial neural networks (ANN) and neuro-fuzzy systems (NFS) were used to predict Iranian EFL learners’ final scores and compare them with scores given by their instructor. Sixty-six students’ scores in an English reading comprehension course comprising of five sub-scores of midterm (out of 40), quiz (out of 60), final (out of 50), class participation (out of 5) and bonus (out of 2) were used for training the systems. Two and three-layer ANNs and an NFS were trained to predict students’ final scores using training data. Researchers compared the students’ final scores given by their instructor and those achieved through the ANNs and NFS. The results showed that the NFS could predict and deliver scores that were closer to the linear sum of students’ scores. Moreover, three-layer ANN had a better performance than the two-layer ANN. According to these results, data mining techniques could deliver an accurate estimate of students' abilities in a particular course.