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Systems thinking skills are crucial for tackling the complex problems of the twenty first century; however, very few studies have explored these skills in the context of mathematics. This study aimed to address this gap by: (1) developing an operational framework for assessing systems thinking skills in mathematics, and (2) exploring the feasibility of using this framework to assess students’ systems thinking skills. The developed operational framework, which was created by extracting key concepts from other disciplines through a comprehensive literature review and synthesizing these ideas for application in mathematics, comprises three subskills: the ability to identify or construct multiple relevant elements, recognize or construct relationships, and analyze or construct a system. The items and coding rubrics developed based on this framework were applied to 357 junior high students, successfully distinguishing different levels of systems thinking skills among students and identifying various student profiles.