In this research, it is aimed to examine the effect of STEM activities developed within the scope of a science course on the inquiry and innovative thinking skills of secondary school 7th-grade students. In this context, quantitative and qualitative research approaches were used together. In the quantitative dimension of the research, the pretest-posttest experimental control group design was preferred among the quasiexperimental designs. In this direction, 2 experimental groups and 2 control groups were formed. STEM activities were carried out in the experimental groups whilst traditional teaching methods were used in the control groups. In the qualitative dimension of the research, the case study was preferred. With the case study, the subject can be examined in-depth, and a broad perspective on the phenomenon can be provided. 144 7th grade students in Kastamonu province determined by a simple random sampling method participated in the research. Four different public schools were chosen so that student groups would not be affected by each other. Through the quantitative and qualitative data collection tools resorted to in this study, inquiry and innovative thinking skills were examined. The Inquiry Skills Scale (ISS) developed by Aldan-Karademir and Saracaloglu (2013) and the Innovative Thinking Tendencies Scale (ITTS) developed by Deveci and Kavak (2020) were used as quantitative data collection tools. Semi-Structured Observation Form (SSOF) developed by Doganay (2018) and Semi-Structured Interview Questions (SSIQ) developed by Deveci and Kavak (2020) and field notes taken by researchers and those of an independent observer were used as qualitative data collection tools. In light of the findings of the research, it was determined that the students' post-test scores and qualitative application results showed a significant difference in favour of the experimental group. As a result of interviews, observations, and field notes, it was observed that students' inquiry skills and innovative thinking tendencies were not at the expected level, but these skills developed positively with STEM activities.