Critical thinking and STEM career perception are important in 21th century and STEM education is necessary to promote middle school students’ critical thinking skills and STEM perception. In this research we aim to research the effects of engineering design-based STEM education on the middle school students’ critical thinking skills and STEM perceptions. In this case study, STEM activities were developed according the subjects of “Reflections in Mirror” and “Absorption of Light” and prepared activity booklet. The activities implemented with 30 seventh grade middle school students in Istanbul province for five weeks (20 course hours). While student solved the design problems in the housing estate and designed “Safe and Eco-Friendly House Estate”, the teacher guided students in this process. To solve the problem/ground design challenge, they did five mini designs and five researches/experiments in six teams of five students. The quantitative data were performed California Critical Thinking Disposition Inventory (CCTDI) and STEM Perception Test as pre and post-test and analysed statically. Semi-structured interviews were performed to support quantitative data and analysed descriptively. STEM education developed students’ critical thinking skills and STEM perceptions positively and also it had indirect effects on their career awareness.