The aim of this study was to identify the effects of GeoGebra software on students' conceptual and procedural knowledge and the achievement of Form Two students in Mathematics particularly on the topic Function. In addition, this study determined the role of procedural knowledge as a mediator between conceptual knowledge and students' achievement. This study employed a quasi-experiment approach on 345 students divided into two groups. A group with 169 students used the GeoGebra software, while another 176 students used the conventional method to learn Mathematics. The data were collected through conceptual and procedural tests, and from students' achievement in the topic Function of the Mathematic examination. The data were analysed using the SPSS 22.0, AMOS 18.0 and ANATES v4 software. Findings of the study show that students who used GeoGebra to learn Mathematics have higher mathematical conceptual and procedural knowledge compared to those who learned Mathematics through the conventional methods. Both experiment groups show that procedural knowledge is a significant mediator between conceptual knowledge and students' achievement in Mathematics. In conclusion, GeoGebra software is capable of enhancing students' conceptual and procedural knowledge, which at the same time significantly improves students' achievement.