Acute liver failure (ALF) is a life-threatening medical condition that often leads to hepatic encephalopathy (HE). Animals and humans with HE have shown elevated cerebrospinal fluid (CSF) levels of glutamine and glutamate, which may be associated with brain impairment. In this study, we aim to evaluate the relationship between blood-brain barrier (BBB) integrity and CSF amino acid levels with the neurological status of rats after subtotal hepatectomy. Adult male Wistar rats underwent a subtotal hepatectomy (removing 92% of hepatic mass or SHAM group) and were divided into 4 (four) cohorts. Animals with ALF presented severe neurological impairment and high mortality rates when compared to the SHAM group (Cohort 1). We performed a hepatic function test 24 hours after subtotal hepatectomy, which demonstrated a significant increase of Aspartate aminotransferase (AST), Alanine aminotransferase (ALT), Total Bilirubin, Direct Bilirubin, Prothrombin time and Ammonia levels in blood (Cohort 2). Additionally, the increase of amino acids, glutamine, and albumin levels in CSF as well as of Evans Blue penetration into the brain tissue was correlated with the neurological grades of HE, indicating signs of impaired BBB permeability induced by ALF (Cohort 3). Furthermore, the animals’ mortality rate showed a positive correlation with the increase of amino acid levels in CSF following subtotal hepatectomy (after 12h, Cohort 4). Our data highlight the potential role of amino acid levels in CSF, especially glutamine, for detection purposes even in the early stages of HE and suggest that these molecules offer prognostic value for patients progressing to coma and death.