© 2020 CSIRO Framelets and their attractive features in many disciplines have attracted a great interest in the recent years. This paper intends to show the advantages of using bi-framelet systems in the context of numerical fractional differential equations (FDEs). We present a computational method based on the quasi-affine bi-framelets with high vanishing moments constructed using the generalized (mixed) oblique extension principle. We use this system for solving some types of FDEs by solving a series of important examples of FDEs related to many mathematical applications. The quasi-affine bi-framelet-based methods for numerical FDEs show the advantages of using sparse matrices and its accuracy in numerical analysis.