The Hermite-Birkhoff (HB) interpolation is an extension of polynomial interpolation that appears when observation gives operational information. Additional capabilities in HB interpolation by considering fractional operators are created, as it occur in many applied systems. Due to the nice properties in kernel-based approximation, we intend to apply it to solve the HB interpolation in the fractional sense. We show the standard basis in kernel-based approximation is often insufficient for computing a stable solution in fractional HB interpolation. Because of the inherent ill-condition of kernel-based methods, we investigate the fractional HB interpolation using alternate Hilbert-Schmidt SVD (HS-SVD) bases, since it provides a linear transformation which can be applied analytically, and therefore, is able to remove a significant portion of the ill-conditioning. Also, the convergence and stability of the fractional HB interpolation using HS-SVD method are discussed. Numerical results show that in solving fractional HB interpolation, although the standard basis for many positive definite kernels is ill-conditioned in the flat limit, the HS-SVD basis solves the existing problem.