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We report the formulation and implementation of an extended Frenkel exciton model (EFEM) designed for simulating the dynamics of multichromophoric systems, taking into account the possible presence of interchromophore charge transfer states, as well as other states in which two chromophores are simultaneously excited. Our approach involves constructing a Hamiltonian based on calculations performed on monomers and selected dimers within the multichromophoric aggregate. Nonadiabatic molecular dynamics is addressed using a surface hopping approach, while the electronic wave functions and energies required for constructing the EFEM are computed utilizing the semiempirical floating occupation molecular orbitals-configuration interaction (FOMO-CI) electronic structure method. To validate our approach, we simulate the singlet fission process in a trimer of 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene (ThBF) molecules, embedded in their crystal environment, comparing the results of the EFEM to the standard “supermolecule” approach.