The present study investigates the influence of a virtual laboratory-based learning kit on the development of clever thinking skills among middle school students engaged in chemistry education. This research responds to the increasing demand for effective and engaging pedagogical approaches within the realm of science education. The study formulates a null hypothesis asserting that there is no statistically significant difference, at the 0.05 significance level, between the average scores of students in the experimental group utilizing the virtual laboratory-based learning kit and those in the control group receiving instruction through traditional methods. An experimental design with partial control was employed, featuring an experimental group comprising 34 students and a control group consisting of 32 students from Qadisiyah Middle School for Boys. Participants were randomly selected to create an unbiased sample of 66 students. The groups were equated based on key variables, such as age, grade 6 grade point average (GPA), and prior knowledge of the subject matter. To facilitate effective learning, twenty-four daily teaching plans were meticulously constructed: the experimental group’s plans were aligned with the virtual laboratory-based educational kit, while the control group adhered to conventional instructional techniques. Subsequent statistical analysis was performed using SPSS to assess the outcomes of the two independent samples with unequal sizes. The findings revealed a significant enhancement in clever thinking skills among students in the experimental group who engaged with the virtual laboratory-based educational kit, in comparison to their counterparts in the control group. In conclusion, the results of this study indicate notable advantages associated with the incorporation of a virtual laboratory-based educational kit into chemistry instruction to foster the development of clever thinking skills among students. This research advocates for the integration of virtual laboratories into pedagogical practices and encourages further investigation across various educational levels and subjects to ascertain their broader implications for learning outcomes.