Background Due to long working hours wearing an N95 mask and PPE kit during the COVID-19 pandemic, the healthcare workers (HCWs) complained of headaches, confusion, and exhaustion. This study was therefore performed to study the changes in brain oxygenation. Aim To compare brain oxygenation in health care workers wearing an N95 mask with a PPE kit versus a three-ply mask during an intensive care setting for 6 hours. Materials and Methods Thirty clinicians and 30 paramedical staff participated in the study. The control (three-ply mask) and subject (N95 mask with PPE) groups included 15 clinicians and 15 paramedical staff. A comparative analysis of brain oxygenation using a 3T magnetic resonance imaging (MRI) machine was performed in these two groups at the beginning and the end of their work shift. Results The mean age of the individuals in the control and subject groups was 30.8 and 30.13 years, respectively. The median value of brain oxygenation in the control and subject groups in the pre-shift was between 33 and 31 and post-shift was 30 and 24. The drop in brain oxygenation in subjects was more than the controls ( p = 0.004) in the post-shift assessments. The cerebral blood flow (CBF) in the bilateral middle cerebral artery (MCA) using arterial spin labeling (ASL) showed a rise in CBF in both groups post-shift as compared with the pre-shift values. The median values of the right and left MCA in the control and subject groups pre-shift were 82.75/83.45 and 89.75/106.65. The post-shift median values of both MCAs of the control and subject groups were 115.65/115.55 and 109.60/119.49. Conclusion MRI-BOLD imaging revealed a significant drop in brain oxygenation in the subject group as compared with the control group. Multiphasic-ASL showed a compensatory rise in CBF in both groups.