Volitionally modifying respiration leads to changes in middle cerebral arterial (MCA) blood flow. The effect of changes in breath rate on MCA blood flow has not been reported. To determine the effect of slow (bumblebee yoga breathing) and fast (high frequency yoga breathing) yoga breathing techniques on MCA blood flow and vagally mediated heart rate variability. Thirty participants (mean age ± standard deviation, 27.3 ± 4.2 years) were assessed on 2 separate days practicing either high frequency yoga breathing (HFYB, breath frequency 54.2/min) or slow frequency bumblebee yoga breathing (BBYB, breath frequency 3.8/min) in random order to determine the effects of changes in breath frequency on MCA hemodynamics. Assessments included transcranial Doppler sonography, vagally mediated heart rate variability (VmHRV), and respiration. Both HFYB and BBYB (i) reduced MCA flow velocities, i.e., peak systolic, end diastolic, and mean flow velocities, and (ii) increased MCA pulsatility indices. There was an increase in VmHRV during BBYB based on increased power in high frequency (HF) and low frequency (LF). LF reflects VmHRV for slow breath frequencies. In BBYB the average breath rate was 3.8 breaths/min. In contrast, VmHRV decreased during HFYB (based on reduced HF power; repeated measures analysis of variance, P < 0.05, all cases). Hence, irrespective of the differences in breath frequency, both HFYB and BBYB appear to reduce MCA flow velocities and increase the resistance to blood flow bilaterally, although the VmHRV changed in opposite directions. MCA velocity and pulsatility changes are speculated to be associated with low global neural activity during yoga breathing.