To compare the effects of different educational methods on short and long-term learning outcomes and to investigate the satisfaction and perception of cleft lip and palate (CLP) education among dental students. The theoretical exam on CLP to determine their baseline level of knowledge was taken by the participants(T0). After the exam, the students were randomly divided into three groups and all students attended a lecture-based traditional education on CLP. Students in the first group (n = 40) received no additional teaching (Group A). Students in the second group (n = 38) received model teaching with 3D-printed models (Group B). The third group (n = 39) was trained in e-learning-supported education (Group C). The theoretical exam was repeated immediately after the education (T1/short-term learning), one week later (T2/early long-term learning), and one month later (T3/late long-term learning), and the effect of the education methods on information level was assessed. In addition, a post-training satisfaction questionnaire was administered to participants of Group B and Group C. Both 3D model-based and e-learning-supported approaches significantly improved immediate knowledge of CLP. However, no significant differences were found in knowledge retention over time between the all methods. A majority of students favored the incorporation of both methods in orthodontic education. While both 3D models and e-learning effectively enhance short-term CLP knowledge among dental students, their long-term educational impacts are comparable. However, student preferences indicated that the use of 3D-printed models and e-learning strategies may be useful augmentations to traditional lecture education.