Early-onset sepsis is one of the leading causes of neonatal morbidity and mortality worldwide and timely diagnosis is, therefore, of paramount importance. As there is a lack of literature regarding early alteration of the cerebral blood flow (CBF) in neonatal sepsis, our study aimed to appraise changes in the CBF velocities and Doppler indices in neonates with early-onset neonatal sepsis (EONS) and to assess its diagnostic accuracy. A total of 99 neonates were recruited in the study; 56 neonates with EONS, and the age-matched 43 neonates without any manifestations of sepsis. A Transcranial Doppler examination and cerebral hemodynamics were assessed in neonates during the first seventy-two hours of life. Doppler indices and CBFV were measured in the anterior cerebral artery (ACA), and middle cerebral artery (MCA), of either side. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy were calculated. A significantly lower resistance in Resistivity (RI) and Pulsatility (PI) indices, a significant high end-diastolic velocity (EDV), and relatively higher peak systolic velocity (PSV) in both ACA and MCA have been documented within 72 hours of birth in neonates with EONS compared to the control group of neonates without sepsis. Our Study revealed that assessment of CBF at early hours of birth by Transcranial Doppler examination showed alteration in cerebral hemodynamics in neonates with EONS with an increase in the CBF and a decrease in the resistance. It can be adopted as a bedside, noninvasive tool with immediate diagnostic value.