Nerve growth factor (NGF) is a neurotrophin that is implicated in the modulation of pain perception. Tanezumab, a humanized monoclonal antibody (mAb) specific for NGF, is highly potent in sequestering NGF and has demonstrated efficacy for treatment of chronic pain in clinical trials. We describe a novel, sensitive immunoaffinity liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for quantitative determination of human serum NGF levels at baseline and after tanezumab treatment. The assay combines magnetic bead-based NGF immunoaffinity enrichment using a non-neutralizing polyclonal antibody followed by digestion and quantitation of a NGF-derived tryptic peptide via high-flow peptide immunoaffinity enrichment and nanoflow LC-MS/MS. Following validation, the assay was employed to measure total NGF concentrations in samples from clinical studies. The assay had a <10% interassay relative error and <15% interassay coefficient of variation across a range from 7.03 to 450 pg/mL human NGF. Generally, human basal serum NGF concentrations were between 20 and 30 pg/mL which, upon treatment with tanezumab, elevated in a dose-dependent manner into the high pg/mL to low ng/mL range. This is the first report of clinical trial implementation of a MS-based assay that uses sequential protein and peptide immunoaffinity capture for protein target quantitation. The use of robotic sample preparation and a robust chromatography configuration enabled this technology to advance into the routine clinical analysis and now provides a bioanalytical platform for the development of similar assays for other protein targets.