This study aims to determine the differences in learning motivation and students' cognitive learning outcomes through the application of augmented reality-based e-learning and 3D animated videos with discovery learning models. This research is a quasi-experimental research with a pretest-posttest nonequivalent control group design. Data collection was only carried out once in a meeting, with material on the digestive system, sub-chapters on the structure and function of the organs that make up the digestive system. The two experimental classes were taught by the same teacher, model, and learning time, but with different treatments, where experimental class 1 was based on augmented reality while experimental class 2 was based on 3D animation video. The instruments used in this study were student learning motivation questionnaires and pretest and posttest questions to measure students' cognitive learning outcomes. The instrument has been validated by experts in the field and is declared suitable for use. In addition, statistical tests on items and questionnaires indicate that the instrument is valid and reliable. The sample of this study consisted of 72 students of SMA Negeri 1 Karanganyar consisting of 36 students of class XI MIPA 5 as the experimental class 1 and 36 students of class XI MIPA 6 as the experimental class 2. The sample was taken using cluster random sampling technique, where the sample was tested for equality with ANOVA test was then randomized per class. The data obtained were then analyzed quantitatively using the Analysis of Covariance (ANCOVA) test with the pretest as a covariate. The results showed that there were differences in students' learning motivation and cognitive learning outcomes between the application of augmented reality-based e-learning and 3D animated videos. Students' learning motivation with the implementation of augmented reality-based e-learning is higher than the application of 3D animated video-based e-learning, as indicated by an average score of 1.03. The cognitive learning outcomes of students with the application of augmented reality-based elearning are also higher than the application of 3D animated video-based e-learning, as indicated by the average score of 24.28.