An efficient 3-step procedure for the synthesis of novel β-pyridinium/quinolinium/bromine-substituted bis(1,3-dimethylbarbituric acid)trimethine oxonol dyes was developed that involves a simple triethylamine-promoted condensation of 1,3-dimethylbarbituric acid with preformed vinamidinium salts. 1H NMR, 13C NMR, IR and mass spectral data confirmed the structures of the dyes. Solutions of the dyes in CH3CN exhibited absorption and fluorescence emission maxima in the range of 467–480 nm and 531–712 nm, respectively, identifying that the dyes show unusually large Stokes shifts (~230 nm). Investigating the photophysical properties of dye 3a in a series of organic solvents with different polarity confirmed intramolecular charge transfer (ICT). Optimized geometries of the synthesized dyes in the ground state calculated using density functional theory (DFT) at the B3LYP/6-311G(d,p) theory level identified that planar cis and trans configurations were preferred for the pyridinium/quinolinium and bromine substituted dyes, respectively. TD-DFT calculations on the dye excited state structures identified that rotation of the bulky pyridinium substituents during relaxation is responsible for the large Stokes shift. The unique properties of the dyes suggest they could find use as fluorescent visualizers for intracellular imaging.