We report the implementation of a symmetry-adapted perturbation theory algorithm based on a density functional theory [SAPT(DFT)] description of monomers. The implementation adopts a density-fitting treatment of hybrid exchange-correlation kernels to enable the description of monomers with hybrid functionals, as in the algorithm by Bukowski, Podeszwa, and Szalewicz [Chem. Phys. Lett. 414, 111 (2005)]. We have improved the algorithm by increasing numerical stability with QR factorization and optimized the computation of the exchange-correlation kernel with its 2-index density-fitted representation. The algorithm scales as O(N5) formally and is usable for systems with up to ∼3000 basis functions, as demonstrated for the C60-buckycatcher complex with the aug-cc-pVDZ basis set. The hybrid-kernel-based SAPT(DFT) algorithm is shown to be as accurate as SAPT(DFT) implementations based on local effective exact exchange potentials obtained from the local Hartree-Fock (LHF) method while avoiding the lower-scaling [O(N4)] but iterative and sometimes hard-to-converge LHF process. The hybrid-kernel algorithm outperforms Hartree-Fock-based SAPT (SAPT0) for the S66 test set, and its accuracy is comparable to the many-body perturbation theory based SAPT2+ approach, which scales as O(N7), although SAPT2+ exhibits a more narrow distribution of errors.