The purpose of this work is to examine the issue of pre-service science teachers' (PSST) Geogebra applications on misconceptions about projectile motion (PM) and the permanence of learning concepts. In this study, quantitative research method was used as scientific research method, and semi-experimental design with pre-test, post-test control group was used as a pattern. The accessible population of this study is PSST who study in a university located in Kayseri, Turkey in the 2019-2020 academic year. Sample of the study included 36 freshman PSST, studying at the university level in Kayseri. 18 of the participants are experimental-group (EG) and 18 of them are control-group (CG). Both groups learned the subject of projectile motion (PM) together in the classroom. In addition to the traditional teaching method, the EG participated eight-week in the Geogebra course based on the conceptual change model and prepared physics simulations with Geogebra. "Conceptual Questions on Projectile Motion" was used as a data collection tool and the data were analyzed by means of statistics (t-test) based on the difference between averages. The results revealed that both the post-test's and permanence test's mean scores of the EG PSST were significantly higher than the mean score of the CG PSST (post-test: t=2.525; p< 0.05) (permanence test: t=5.466; p< 0.05). Furthermore, in this study, many misconceptions about the PM were identified.