Venous thromboembolism (VTE) (deep vein thrombosis and its complication, pulmonary embolism) is a major cause of morbidity and mortality in hospitalized patients and about 7% of these cases are due to immobility secondary to a neurological impairment. Acquired brain injury (ABI) has also been recognized as one of the main risk factors for VTE. Numerous epidemiological studies have been conducted to assess the risk factors for VTE in institutionalized polytrauma patients, although there is a lack of information about neurorehabilitation wards. Since VTE is often undiagnosed, this prospective study aimed to determine the prevalence and clinical characteristics of lower-limb deep venous thrombosis (DVT) in ABI patients at neurorehabilitation admission. Methods: ABI patients were screened for DVT on admission to the intensive rehabilitation unit (IRU) with compression ultrasonography and basal D-dimer assay and were daily clinically monitored until discharge. A total of 127 consecutive ABI patients (mean age: 60.1 ± 17.6 years; 63% male; time from event: 30.9 ± 22.1 days; rehabilitation time in IRU: 84.6 ± 58.4 days) were enrolled. Results: On admission to the IRU, the DVT prevalence was about 8.6%. The mean D-dimer level in patients with DVT was significantly higher than in patients without DVT (6 ± 0.9 vs. 1.97 ± 1.61, p-value = 0.0001). ABI patients with DVT did not show any significant clinical characteristics with respect to ABI without DVT, although a prevalence of hemorrhagic strokes and patients originating from the Intensive Care Unit and Neurosurgery ward was revealed. During the rehabilitation period, patients with DVT showed a significant difference in pharmacological DVT prophylaxis (high prevalence of nadroparin with 27.3% vs. 1.7%, p-value = 0.04) and a prevalence of transfers in critical awards (36% versus 9.5% of patients without DVT, p-value = 0.05). The mortality rate was similar in the two groups. Conclusions: Our research offers a more comprehensive view of the clinical development of DVT patients and confirms the prevalence rate of DVT in ABI patients as determined upon IRU admission. According to our findings, screening these individuals regularly at the time of rehabilitation admission may help identify asymptomatic DVT quickly and initiate the proper treatment to avoid potentially fatal consequences. However, to avoid time-consuming general ultrasonography observation, a more precise selection of patients entering the rehabilitation ward is required.