Background Study: The effects of the flipped classroom (FC) on students' academic performance remain ambiguous, and the use of pre-class videos may be one of the main factors hindering students' progress. A software package called GeoGebra has been proposed as a substitute for pre-class videos to aid students' learning. Objective: This study investigates the effect of the FC using GeoGebra (FCG) on mathematical performance and memory among senior secondary students. Methods: One hundred and sixty students of a senior high school in China were selected. A quasi-experimental design was implemented in which the classes were split into the intervention group (FCG), control group A (FCV) and control group B (TL) by random assignment. Pretest, Post-test 1 and Post-test 2 were introduced. Results and Conclusion: The results indicate that both the FCG and the FC with pre-class videos (FCV) were more effective than traditional lectures in enhancing students' academic test scores, and that the effect of the FCG was comparable to its video counterpart, F(2, 136) = 3.752, ρ = 0.026, η ² = 0.052. Although their effects were similar, the qualitative results revealed some hidden benefits associated with the replacement of pre-class video with GeoGebra. Furthermore, although they were equally effective in promoting students' performance in the short-term, the long-term effects on academic performance of both forms of FC were non-significant when compared with traditional lectures.