The relationship between gender and educational outcomes is still very interesting to talk about. This study aims to test the effectiveness of the probing prompting learning model on the physics concept mastery, the effect of gender on the physics concept mastery and examine the interaction between the application of the probing prompting learning model and discovery learning in terms of gender on the students’ physics concept mastery. The research method used is quasi-experiment with a post-test only control group design. The research sample consisted of two classes chosen by purposive sampling technique; class VIII A as the experimental class and class VIII B as the control class. Data collection techniques used were test to obtain the data of concept mastery. The hypothetical test used was two-way ANOVA. The conclusions from the results of this study are: (1) The probing prompting learning model is more effective than the discovery learning model on students’ physics concept mastery, (2) gender affects the students’ physics concept mastery, and (3) there is no interaction between the application of the probing prompting learning model and discovery learning in terms of gender toward the students’ physics concept mastery.