Purpose This study aimed to determine differences according to age groups and gender in the parameters of aqueductal cerebrospinal fluid (CSF) flow in childhood using phase-contrast cine magnetic resonance imaging (MRI) method. Materials and methods This prospective study included 47 boys and 36 girls for a total of 83 healthy children. The cases were divided into three groups depending on age as infants (1–12 months), children (12–120 months), and adolescents (120–204 months). To quantitatively evaluate CSF flow, images in the transverse plane were taken at the cerebral aqueduct level using the phase-contrast MR angiography technique in a 1.5-T MR unit. Peak and average velocity (cm/s), cranial direction, caudal direction and net volume (ml), and aqueduct area (mm2) were calculated. To assess differences between the groups, a one-way analysis of variance and least significant difference tests were used. Results A statistically significant difference was determined between children and adolescents in peak velocity and caudal direction volume (P=.012 and P=.039, respectively) and between infants and children in cranial direction volume (P=.036). Peak velocity, cranial direction, and net volume were higher in boys (P=.050, P=.016, and P=.029, respectively). There were no differences by age and gender in the aqueduct area. Conclusion In conclusion, this study determined the normal values for the CSF flow parameters of velocity, volume, and aqueduct area using phase-contrast MRI in healthy children. Velocity and volume parameters varied according to age and sex and were not affected in the aqueductal area.