Perylenediimide (PDI) derivatives have emerged as potential candidates for efficient energy and charge transport materials, particularly in organic photovoltaics and singlet exciton fission applications. A lot of effort has been devoted to understand efficient coherent energy transfer in light harvesting systems in nature and to develop organic molecules for artificial photosynthesis. Perylene is one of the biomimetic alternatives to chlorophyll a for use in energy donor–acceptor systems. Photoinduced energy transfer in PDI cluster systems leads to delocalization of charges in the molecules and competes with charge localization process caused by structural distortion. This competition has a profound effect on achieving the desired properties of a molecule for further applications. Therefore, controlling the energy transfer dynamics by adjusting the underlying chemical structure and the surrounding environment is a crucial task. In the present work, we compared the energy transfer dynamics of three different PDI tetramer molecules, SF-PDI4, BFE-PDI4, and AD-PDI4, by femtosecond time-resolved fluorescence anisotropy spectroscopy, and discussed the role of the core structures in tetramers. Along with theoretical calculations, we provided simulations using Förster theory for concurrent energy transfers within the tetramers. As a result, molecular structures by quantum mechanical calculations and Förster theory nicely reproduce the experiment.