Growing evidence suggests that pathophysiological mechanisms leading to neurodegeneration and neuronal loss take place during the chronic phase of a severe traumatic brain injury (TBI). In this study we evaluated a well-established marker of brain injury, the neuron-specific enolase (NSE), in the serum of 51 patients with severe TBI (86% males, mean age 33.8 ± 11.1 years). All patients' samples were available from a previous study and the mean time between TBI and blood sample collection was 23.2 ± 31.5 months (28 patients were evaluated within 12 months of TBI and 23 patients were evaluated ≥12 months after TBI). Patients' NSE levels were compared with those obtained from 30 age and sex-matched healthy controls (87% males, 33.7 ± 11.3 years). We found that NSE levels were significantly lower in patients (median 3.2 ng/mL; 25th, 75th percentile 2.5, 5.1) than in healthy controls (median 4.1 ng/mL; 25th, 75th percentile 3.1, 7.5) (p = 0.026). This finding was mainly driven by data from the chronic patients, that is, those who experienced their TBI at least 12 months before the evaluation. Indeed, these patients had significantly lower NSE levels (median 2.6 ng/mL; 25th, 75th percentile 1.9, 4) than healthy controls (p < 0.01). On the other hand, NSE levels evaluated in patients <12 months from TBI (median 3.9 ng/mL; 25th, 75th percentile 2.8, 5.7) did not significantly differ from controls (p = 0.3). These findings possibly reflect a progressive brain atrophy with reduced baseline NSE release in the chronic phase of a severe TBI.