Background: Nerve growth factor (NGF) plays essential roles in epithelial repair, neuro-immune signalling, and inflammatory pain. However, its dynamic changes during autologous peripheral stem cell transplantation (APSCT) and the relationship to transplant-related mucosal and systemic injury remain poorly understood. The present study aimed to characterize longitudinal alterations in salivary and serum NGF levels during APSCT and to compare them with age-sex matched healthy controls. Materials and Methods: Ten patients with malignant hematological diseases undergoing APSCT were enrolled. Salivary and serum NGF concentrations were measured at four clinically relevant time points: pre-conditioning (Day −3/−7), transplantation day (Day 0), early post-transplant nadir (Day +7), and mucosal recovery phase (Day +14). Healthy controls included volunteers aged 25–34 (n=9), 35–59 (n=7), and ≥60 years (n=7). NGF levels were quantified by ELISA and compared across stages and age groups. Results: Both salivary and serum NGF in APSCT patients showed elevation, with significant increases at Day 0 and a second, more pronounced peak at Day +7, followed by a decline toward recovery by Day +14. This NGF surge paralleled the expected trajectory of conditioning-induced tissue injury and peak post-transplant mucositis. In healthy controls, NGF concentrations in both serum and saliva decreased with age, with the ≥60-year group exhibiting significantly lower baseline levels than younger groups. Conclusions: APSCT induces marked and stage-specific elevations in NGF, likely reflecting acute chemotherapeutic injury, inflammation-driven neuro-immune activation, and subsequent tissue repair responses. The second NGF peak at Day +7 coincides with the nadir phase and the period of greatest mucosal damage, suggesting a potential role for NGF as a biomarker of transplant-related mucosal and systemic stress. Together, these findings highlight NGF as a promising candidate for monitoring tissue injury and recovery in APSCT.