Extended exposure to radiation, microgravity, and isolation during space exploration has significant physiological, structural, and psychosocial effects on astronauts, and particularly their central nervous system. To date, the use of brain monitoring techniques adopted on Earth in pre/post-spaceflight experimental protocols has proven to be valuable for investigating the effects of space travel on the brain. However, future (longer) deep space travel would require some brain function monitoring equipment to be also available for evaluating and monitoring brain health during spaceflight. Here, we describe the impact of spaceflight on the brain, the basic principles behind six brain function analysis technologies, their current use associated with spaceflight, and their potential for utilization during deep space exploration. We suggest that, while the use of magnetic resonance imaging (MRI), positron emission tomography (PET), and computerized tomography (CT) is limited to analog and pre/post-spaceflight studies on Earth, electroencephalography (EEG), functional near-infrared spectroscopy (fNIRS), and ultrasound are good candidates to be adapted for utilization in the context of deep space exploration.