Body awareness, which comprises the sense of body possession and action ownership, is essential for the adaptive movement of humans in response to external environments. However, existing body cognition assessments include many overt elements of cognitive functional activity, but no assessment captures the latent body cognition necessary for exercise and daily life activities. Therefore, this study aimed to devise a body cognition assessment system (BCAS) to examine the functional basis of body cognition in healthy participants and investigate its usefulness. The BCAS was used to assess body cognition on three occasions, and BCAS values were calculated from the results of the assessment. The intraclass correlation coefficient (ICC) was used to determine reproducibility. Neural activity in the brain during somatocognition assessment while conducting the BCAS was measured by electroencephalogram. Moreover, the functional basis for somatocognition with the BCAS was also investigated. The results demonstrated that the BCAS values varied across the three administrations (ICC (1.3) = 0.372), and changes in the state of neural activity in the brain were observed. The results suggest that assessment using the BCAS may be a new indicator of ever-changing body cognition.