This research aimed to explore the effect of problem-based STEM activities on middle school students' perceptions related to problem-solving skills and their critical thinking tendencies. The sample consisted of 81 students. A mixed method was employed in the research. The quantitative data collection tools were the "Critical Thinking Tendency Scale" and "The Perception Scale for Problem Solving Skill." The qualitative tools were a Semi-structured Interview Form and Experience diaries developed by the researcher considering the quantitative scales. While the quantitative data, obtained in the research, were analyzed with one-way ANOVA, the statistical method; and the qualitative data were analyzed with the content analysis. At the end of the research, a significant difference was detected in favor of experimental groups in the students' perceptions of their problem-solving skills and critical thinking tendencies. On the other hand, in the qualitative results, it was reported that the problem-based STEM education created a positive effect as cognitive maturity and innovativeness in the students' feelings, thought, and behaviors. It was concluded that the students used the inter-disciplinary knowledge with the problem-based STEM activities; found the problem solving, understanding the problem and working with their friends favorably. According to these results, it can be claimed that STEM education is highly effective in developing the skills that are expected from individuals in the 21st century such as problem-solving, critical thinking, and social interaction.