In this study, we consider regular eigenvalue problems formulated by using the left and right standard fractional derivatives and extend the notion of a fractional Sturm–Liouville problem to the regular Prabhakar eigenvalue problem, which includes the left and right Prabhakar derivatives. In both cases, we study the spectral properties of Sturm–Liouville operators on function space restricted by homogeneous Dirichlet boundary conditions. Fractional and fractional Prabhakar Sturm–Liouville problems are converted into the equivalent integral ones. Afterwards, the integral Sturm–Liouville operators are rewritten as Hilbert–Schmidt operators determined by kernels, which are continuous under the corresponding assumptions. In particular, the range of fractional order is here restricted to interval (1/2,1]. Applying the spectral Hilbert–Schmidt theorem, we prove that the spectrum of integral Sturm–Liouville operators is discrete and the system of eigenfunctions forms a basis in the corresponding Hilbert space. Then, equivalence results for integral and differential versions of respective eigenvalue problems lead to the main theorems on the discrete spectrum of differential fractional and fractional Prabhakar Sturm–Liouville operators.