Philip Bunker's published scientific work has focused on the use of fundamental quantum mechanics to predict and interpret the spectral properties of polyatomic molecules due to their combined rotational, vibrational, electronic and nuclear-spin states, and their symmetries. He has been particularly concerned with the study of the energy levels and spectra of molecules that undergo large amplitude vibrational motions. Applications of this work to the methylene (CH) molecule proved to be
important in determining the separation between the singlet and triplet electronic states, and in determining which singlet and triplet rotational levels interact. In the 1990s, he returned to the problem of determining the torsional barrier in 
dimethylacetylene after Robert McKellar and John Johns, experimentalists at the National 
Research Council of Canada, had obtained a very high resolution infrared spectrum of the molecule.
Bunker is a well-known expert in the use of the molecular symmetry group. At the end of Longuet-Higgins' paper in which he introduced permutation and permutation-inversion molecular symmetry groups, Longuet-Higgins wrote: "In conclusion it should be added that the present definition can be extended to linear molecules, and to molecules where spin-orbit coupling is strong; but these topics are best dealt with separately." However, a few years later (in 1967) Longuet-Higgins left the field of theoretical chemistry; he wrote nothing more about molecular symmetry and did not make these extensions.  Bunker then developed the extensions of these principles to linear molecules as well as to molecules with strong spin-orbit coupling Bunker is also known for his work in the quantitative description of non-adiabatic effects in quantum molecular dynamics.
Together with Per Jensen (1956-2022), who was a theoretical chemist at Bergische Universität Wuppertal, Bunker has written two books on theoretical chemistry and molecular spectroscopy; Molecular Symmetry and Spectroscopy (1998) and Fundamentals of Molecular Symmetry (2005).
Currently, Bunker is Researcher Emeritus at the National Research Council of Canada and a guest scientist at the Fritz-Haber Institute of the Max Planck Society. He has also held visiting scientist positions at universities and institutions around the world during the course of his career, including ETH-Zurich, Massey University, Kyushu University and University of Florence. During the course of his career he has delivered over 400 invited 
lectures.