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This study investigated how integrating GeoGebra into classroom teaching may affect high school students’ learning of algebra. One hundred and four ninth-grade Chinese students participated in this research, where they were randomly assigned to either the experiment or control group. While the former were taught with GeoGebra on fundamentals of functions, the latter were taught by the same teacher in a traditional manner. Over the span of eight weeks, the experiment group improved significantly more than the control group in both conceptual understanding and competence in applying effective learning strategies. Nonetheless, no significant difference was found in their learning motivation. This work has important implications for future research about impacts of employing mathematics software on different aspects of learning.