(1) Background: Osteonecrosis (ON) of the femoral head is a disabling disease for which limited treatment options exist. Identifying therapeutic targets of its evolution could provide crucial insights into multi-targeted approaches. The aim of this pilot study was to assess the histopathological features of patients with non-traumatic femoral head (NTFH) and post-traumatic femoral head (PTFH) ON to produce a fresh vision for clinical use. (2) Methods: We got biopsies from patients with different ON stages, according to the ARCO system. Samples from multi-organ donors were used as controls. Histological and immunohistochemical evaluations were performed on the osteochondral unit. (3) Results: The PTFH group displayed several fibrotic reactions, a small stem cell pool and a lower international cartilage repair society (ICRS)-I score than NTFH, which instead presented intact cartilage similar to the controls. Immunostaining for collagen I and autotaxin confirmed these features in the PTFH group, which displayed top levels of MMP-13 involved in cartilage loss and reduced CB-2 in the underlying bone. Both groups manifested a similar pattern of apoptotic and pain mediators. (4) Conclusions: The different histopathological features suggest a multi-disciplinary and multi-targeted approach for ON. Further studies are necessary to measure the effect size to gain clinical evidence.