Although the mechanisms of neurological disorders after cardiac surgery in neonates are still not fully understood, alterations in blood flow after cardiopulmonary bypass (CPB) may lead to cerebral injury. The aim of the study was the analysis of flow changes in the carotid artery of neonatal piglets after CPB. Ten neonatal piglets (younger than 7 days) were connected to the CPB and further management underwent three steps: (i) cooling to 32°C core temperature within 30 min; (ii) cardiac arrest under cardioplegic myocardial protection for 90 min; and (iii) rewarming to 37°C after cross-clamp release (60 min of reperfusion). In summary, piglets were separated from CPB after a total duration time of 180 min. The blood flow was measured in the left carotid artery by an ultrasonic flow probe before CPB (baseline), immediately after CPB, 30 min, and 60 min after CPB. Additionally, the pulsatility index and the resistance index were calculated and compared. Finally, the relation of the carotid artery flow data with the corresponding pressure data at each time point was compared. After termination of CPB, the carotid artery mean flow was reduced from 28.34 ± 13.79 mL/min at baseline to 20.91 ± 10.61 mL/min and remained reduced 30 and 60 min after CPB termination (19.71 ± 11.11 and 17.64 ± 15.31 mL/min, respectively). Both the pulsatility and the resistance index were reduced immediately after CPB termination and increased thereafter. Nevertheless, values did not reach statistical significance. In conclusion, the carotid Doppler flow immediately after CPB and mild hypothermia in neonatal piglets was lower than before CPB due to reduced vascular resistance. Additionally, the pressure–flow relation revealed that immediately after CPB, a higher pressure is required to obtain adequate flow.