Photofragmentation of thymine and 5-bromouracil into cation and neutral fragments following the core ionization by soft x-rays using photoelectron-photoion-photoion coincidence technique has been studied. The fragment ion mass spectra were recorded in coincidence with the C 1s photoelectron spectra. In the case of thymine, deuterated samples were used to identify fragments. Deuteration or bromination allowed us to study not only the main fragmentation channels of these pyrimidine bases, but also to investigate if replacement of an exocyclic functional group affects molecular fragmentation. We found that the dominant fragmentation channels involve only one starting geometry, and the base ring and other bond cleavages, leading to the detected fragments, are essentially identical between thymine and 5-bromouracil. In addition, the relative intensities of the strongest fragmentation channels were determined and compared with calculated appearance energies using ab initio unrestricted Hartree-Fock theory.