Different methodologies have arisen in the last century, and all of them advocate for a change of the traditional method. In this paper, Inquiry-Based Learning is introduced in an experimental group (17 students) to see the different results of children following this innovative method as compared to the control group (16 students) that followed the traditional method. The participants of the study are doing the third year of Primary Education in Spain. The assessment results showed that although just after the post-test both groups did not have significant differences, they became more prominent when the test was repeated in a couple of weeks. This suggests that inquiry-based learning is a better methodology to teach Science due to the students’ significant learning, their interest and motivation, and the academic results achieved. The biggest problem we are concerned with is if children acquire the knowledge or it is just because they study to pass the exams.