An unprecedented turn in educational pedagogies due to the COVID-19 pandemic has significantly affected the students’ learning process worldwide. This article describes developing a STEM-based online course during the schools’ closure in the COVID-19 epidemic to combat the virtual science classroom’s limitations that could promise an active STEM learning environment. This learning model of the online STEM-based course successfully developed and exercised on 38 primary–preparatory students helped them to overcome the decline in their learning productivity. Various digital learning resources, including PowerPoint presentations, videos, online simulations, interactive quizzes, and innovative games, were implemented as instructional tools to achieve the respective content objectives. A feedback mechanism methodology was executed to improve online instructional delivery and project learners’ role in a student-centered approach, thereby aiding in the course content’s qualitative assessment. The students’ learning behavior provided concrete insights into the program’s positive outcomes, witnessing minimal student withdrawals and maximum completed assignments. Conclusions had been drawn from the course assessment (by incorporating both synchronous and asynchronous means), student feedback, and SWOT analysis to evaluate the course’s effectiveness.