This study aimed to investigate the effect of web-based collaborative learning method with Scratch software on the critical thinking skills of 5th grade students and to create materials in Scratch software on the biodiversity subject. This study, in which a quasi-experimental design with pre-test - post-test control group was used, was carried out with 96 fifth grade students selected using convenient sampling method. In the implementation of the study, in addition to the education and training activities on biodiversity in the control groups, the students in the experimental group created products using the web-based collaborative learning method with Scratch in science and information technologies and software courses. As a result of the t-test for the independent samples of the post-test data obtained from the critical thinking questionnaire, it was determined that the critical thinking skills of the experimental group students were higher than the control group students. It is recommended for younger individuals to use Scratch to come up with solutions by using critical thinking skills to cope with complex problems affecting the whole world such as global warming, wars, and pandemics, and to choose the right solution amongst the given ones. Teachers can get an idea about students’ opinions, conceptual errors, and their capability to express themselves, and they can reorganize the educational activities by taking these variables into consideration.