Computational thinking is an ability which is considered to be essential for the process of problem solving in every science. The current empirical research aims to study the impact of a STEM content Inquiry based scenario using computational tools and educational games, regarding computational thinking (CT) and confidence for “computers use” of 115 students of Greek public schools of the 5th-6th grade. For the needs of this research, a didactic scenario was developed and implemented, using computational tools, such as the Arduino microcontroller, RGB Led’s while a computational model was designed and implemented. The assessment of computational thinking improvement and confidence for computers use was conducted with the use of questionnaires that were administered before and after the intervention. The findings indicate a positive influence of the intervention on the dimensions of computational thinking in the experimental group. The findings can be applied to educational settings that integrate STEM in the teaching sequence in order to enhance students’ confidence with computational experiments.