In education, the use of information, computers, and the Internet as a form of blended technology has been receiving increased attention and consideration. Additionally, increasing attention is being paid toward a scaffolding mechanism that can be integrated into science classrooms in order to solve technological challenges. This work describes a computer-based blended and scaffolding learning toolbox to support numerical concepts for flipped science education, particularly one which is developed and implemented in a MATLAB environment and framed in Adobe Captivate 6 as a HTML5-based e-Learning application, which can be used for science laboratory exercises. This toolbox, named SciEduFIT, is one of the blended and scaffolding learning systems available for use in science education. Through this toolbox, students can acquire the skills to establish the numerical concepts in a flipped science classroom. A survey was conducted to measure the suitability of the proposed toolbox, specifically A to E screens of SciEduFIT. The positive results of the survey indicate that this novel toolbox should be introduced into science classrooms in order to supplement other existing tools currently in use in the area of flipped science education. Therefore, the research shows a general positive perception of the toolbox and highlights the feasibility of the toolbox to achieve significant science learning.