Aim: To study the comparative molecular interactions of Carvacrol and Imatinib with the active sites of Breakpoint Cluster Region (BCR)-Abelson (ABL) fusion protein using molecular docking analysis for the selective anti-Chronic myeloid leukemia (CML) activity. Materials and Methods: In the current study, the binding affinity and the type of molecular interaction between the Carvacrol and the active site amino acid residues of BCR-ABL fusion protein was studied in comparison with known BCR-ABL inhibitor Imatinib. The sample size was calculated by keeping pretest G power 80%. The sample size per group is 10 (N=10) and total sample size is 20. The protein structure of BCR-ABL fusion protein was collected from the protein data bank (PDB) website and the ligand structures were collected from the NCBI-PUBCHEM website. The binding energy (kcal/mol) was calculated using Autodock Vina Software. Results: The mean binding affinity of Imatinib was -10.22 kcal/mol and Carvacrol was -7.46 kcal/mol towards the active sites of BCR-ABL fusion protein. There was a significant (p=<0.001, p<0.001, 2-tailed t-test) difference between the mean binding affinities of Carvacrol and Imatinib towards the active sites of BCR-ABL fusion protein. Carvacrol interacts with active site amino acid residues via both hydrogen and hydrophobic interactions. Conclusion: Though the binding affinity of Carvacrol was significantly less than Imatinib, Carvacrol may bind selectively to the active sites of BCR-ABL fusion protein. Hence, Carvacrol may attach specifically to the CML cells and inhibit their proliferation and could be used as a novel anti-CML agent to treat CML.