Many genetic markers have been associated with variations in treatment response to analgesics, but none have been assessed in the context of combination therapies. In this study, the treatment effects of nortriptyline and morphine were tested for association with genetic markers relevant to pain pathways. Treatment effects were determined for single and combination therapies. A total of 24 functional Single Nucleotide Polymorphisms (SNPs) were tested within the gene loci of OPRM1, ABCB1, CYP2C19 and CYP2D6, COMT and HTR2A. Genotyping was performed in a population of neuropathic pain patients that previously participated in a clinical trial. For monotherapy, neither nortriptyline nor morphine responses were associated with SNPs. However, for nortriptyline + morphine combination therapy, the SNP rs1045642, within the drug efflux pump ABCB1 transporter significantly predicted analgesic response. The presence of the C allele accounted for 51% of pain variance in this subgroup in response to combination treatment. The T-allele homozygotes demonstrated only 20% improvement in pain scores, while the C-allele homozygotes 88%. There was no significant contribution of rs1045642 to the medication side-effects under all treatment conditions. The UK Biobank dataset was then used to validate this genetic association. Here, patients receiving similar combination therapy (opioid + tricyclic antidepressant) carrying the C allele of rs1045642 displayed 33% fewer body pain sites than patients without that allele, suggesting better pain control. In all, our results show a robust effect of the rs1045642 polymorphism on response to chronic pain treatment with a nortriptyline + morphine combination.