Abstract With growing evidence signifying the impact of cerebrospinal fluid (CSF) flow in facilitating waste clearance from the brain and potential pathophysiological links to neurodegenerative disorders, it is of vital importance to develop effective methods to modulate CSF flow in the brain. Here, we attempt this by means of simple commonly used respiratory challenges—paced breathing and breath holding. Functional Magnetic Resonance Imaging scans of the brain and neck respectively were used to record the craniad and caudad CSF movements at the fourth ventricle from eight healthy volunteers during paced breathing and breath holding. Further, we utilized a novel approach for the first time to combine these separately acquired unidirectional CSF movement signals to compare the CSF flow in both directions (in the fourth ventricle) with the respiratory stimuli as a physiological control. Our results demonstrate that these respiratory challenges enhance the magnitude as well as control the direction of CSF movement in the fourth ventricle. They also reveal the capability of blood CO2 concentration changes (induced by respiratory challenges) in the low-frequency range to bring about these CSF movement modulations. Finally, we also successfully report our novel approach where we use these breathing challenges as a unique control condition to detect the small net CSF flows from independently captured unidirectional signals.