Background: Interfacility neonatal transport is essential for regionalized perinatal care, yet its effects on systemic immune responses remain poorly characterized. This study evaluated longitudinal changes in hematologic and inflammatory biomarkers during neonatal transport and investigated the influence of transport modality on these responses. Methods: In this prospective observational study, 161 neonates undergoing air or ground transport to Level III/IV neonatal intensive care units were evaluated at three time points: before transport (T0), immediately after transport (T1), and 12 hours after admission (T2). Physiological stability parameters, complete blood count variables, and inflammatory indices, including neutrophil-to-lymphocyte ratio (NLR), systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), and mean corpuscular volume-to-lymphocyte ratio (MCVL), were analyzed using repeated-measures and mixed-effects models adjusted for transport duration, sedation, and physiological stability. Results: Physiological stability was maintained throughout transport, with no significant changes in heart rate, oxygen saturation, or body temperature. In contrast, significant longitudinal changes were observed in leukocyte populations and inflammatory indices. Total leukocyte and neutrophil counts decreased over time, whereas lymphocyte counts increased. Mixed-effects analyses identified significant effects of time, transport modality, and Time × Transport interaction for WBC, neutrophils, lymphocytes, NLR, SII, and SIRI. These associations remained significant after adjustment for clinical and physiological confounders. MCVL also demonstrated significant effects of time, transport modality, and their interaction, emerging as a potential novel marker of transport-related immune adaptation. Conclusions: Neonatal transport is associated with significant hematologic and immune adaptations despite preserved physiological stability. Air and ground transport induce distinct patterns of leukocyte redistribution and inflammatory responses. MCVL may represent a promising biomarker of transport-related immune adaptation and warrants further investigation in neonatal transport medicine.