Sepsis-associated encephalopathy (SAE) is a common organ dysfunction in patients with severe sepsis or septic shock and leads to higher mortality and longer hospital stay. The diagnosis remains an exclusion process; none of the available measurements are specific for SAE. The aim of the presented prospective and controlled clinical study was to evaluate the possible role of molecular acoustics in determining acute brain injury in septic patients using an acoustocerebrography (ACG) system. ACG is a multifrequency, transcranial ultrasound method that measures the attenuation and time of flight to detect changes in the brain tissue. After approval from the local research ethics committee (of the University Hospital of Rostock: Reg. No.: A 2016-0026), 20 patients were included in two study groups: septic shock group (SG) and control group (CG; postoperative nonseptic patients). All patients were screened several times with the ACG on different days. Blood parameters of organ function, sepsis-related organ failure assessment score, and delirium scores [Confusion Assessment Method for the Intensive Care Unit (CAM-ICU) and Intensive Care Delirium Screening Checklist (ICDSC)] were obtained as well. A neurologist examined all patients at inclusion. Predictive analysis was done using a data-driven statistical method and by deriving a parameter from the ACG data. The study was registered under “clinicaltrials.gov” (Reg. No.: NCT03173196). All patients in the SG were CAM-ICU-positive at inclusion (ICDSC: in mean 4.0) and had clinical signs of SAE. In contrast, all patients in the CG were CAM-ICU-negative, with an ICDSC score of 0. Predictive analysis using the ACG data presented an accuracy of 83.4% with a specificity of 89.0% and a sensitivity of 75.1%. The ACG method may be helpful for the monitoring and diagnosing acute brain injury; however, the results of this first report should be verified by further clinical studies. Further investigations should include long-established instruments of SAE diagnosis, e.g., electroencephalography, MRI, and biomarkers, to compare the results with the ACG measurements.