Boron-dipyrromethene (BODIPY) chromophores have a wide range of applications, spanning areas from biological imaging to solar energy conversion. Understanding the ultrafast dynamics of electronically excited BODIPY chromophores could lead to further advances in these areas. In this work, we characterize and compare the ultrafast dynamics of halogenated BODIPY chromophores through applying two-dimensional electronic spectroscopy (2DES). Through our studies, we demonstrate a new data analysis procedure for extracting the dynamic Stokes shift from 2DES spectra revealing an ultrafast solvent relaxation. In addition, we extract the frequency of the vibrational modes that are strongly coupled to the electronic excitation, and compare the results of structurally different BODIPY chromophores. We interpret our results with the aid of DFT calculations, finding that structural modifications lead to changes in the frequency, identity, and magnitude of Franck-Condon active vibrational modes. We attribute these changes to differences in the electron density of the electronic states of the structurally different BODIPY chromophores.