This study examined the effect of using Monoscopic Three-Dimensional (M3D) and Stereoscopic Three-Dimensional (S3D) animation on students' achievement and perceptions. A total of 66 ninth-grade students participated in this Explanatory Sequential Mixed Design study. At the beginning of the study, an academic achievement test was applied, and then at the end of the study the same academic achievement test, plus an animation opinion scale, an animation rubric, and a structured interview form were applied to both groups. T-test, descriptive statistics, and content analysis were used for the data analysis. The results showed a significant difference in the post-test scores in favour of the students using the S3D animation. Both groups of students provided positive feedback concerning the use of animations in their course; however, they highlighted that S3D animations were more effective and enjoyable. Conclusively, this study is expected to contribute to the limited literature and open a new window for future studies. Additionally, this study may guide instructors towards increasing the effectiveness and efficiency of their instruction within courses that require visual input and scaffolding.