In the present study alkyl-pi interactions between methane and the pyrimidine heterocyclic systems have been studied. Interaction energies were calculated using the B97D/def2-TZVPP level of theory. Energy decomposition analysis (EDA) using SAPT0/ jun-cc-pVTZ method revealed that the interaction energy is mainly dispersion and electrostatic with a minor contribution from induction energy. Non covalent index analysis was performed to visualize the interactions between the fragments of the studied complexes and atoms in molecule (AIM) study were done to investigate the bond critical points (BCP). The natural bond order (NBO) analyses were carried out to study the donor-acceptor orbitals and the second-order perturbation energies. Interaction energy, AIM study and NBO analysis revealed that the alkyl-pi interactions involving the pyrimidine heterocyclic systems become stronger with the presence of various substituents on the pyrimidine ring.