Outcomes in myelofibrosis (MF) patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) appear unaffected by the intensity of the preparative regimen, defined traditionally as myeloablative (MAC) or reduced intensity conditioning (RIC). The Transplant Conditioning Intensity (TCI) index is an objective tool offering a precise measure of conditioning intensity. We explored the potential association between TCI score and overall survival (OS), progression-free survival (PFS), cumulative incidence of relapse (CIR) and non-relapse mortality (NRM) in 2454 MF patients undergoing allo-HCT between 2012 and 2021, selected from the EBMT registry. Patients receiving TCI-intermediate/high regimens had similar OS (HR 1.12, 95% CI 0.97-1.30) and PFS (HR 1.00, 95% CI 0.88-1.14) compared to TCI-low regimens. However, TCI-intermediate/high regimens were associated with lower risk of relapse (HR 0.74, 95% CI 0.61-0.91, p = 0.008) and higher risk of NRM (HR 1.24, 95% CI 1.04-1.48, p = 0.02). Our findings suggest that the TCI score provides a more clinically relevant stratification of conditioning intensity than the conventional MAC/RIC classification. While higher intensity TCI regimens are associated with lower RI, this benefit is offset by increased NRM, resulting in no survival advantage. However, the TCI index may enable a more personalized approach to conditioning regimen selection by balancing relapse risk with patient frailty.