Although it is a normal involution process in advanced age, brain atrophy—also termed atrophic encephalopathy—can also occur prematurely in childhood as a consequential effect of brain tissues injury through trauma or central nervous system infection, though in both normal and premature occurrences this condition always presents with loss of volume relative to the skull. A common tool for the functional study of brain activities is an electroencephalogram, but analyses of this have reportedly identified mismatches between qualitative and quantitative forms, particularly in the use of Delta-alpha ratio (DAR) indices, meaning that the values may be case dependent. The current study thus examines the value of Focused Occipital Beta-Alpha Ratio (FOBAR) as a modified biomarker for evaluating brain functional changes resulting from brain atrophy. This cross-sectional design study involves 260 patients under 18 years of age. Specifically, 207 patients with brain atrophy are compared with 53 control subjects with CT scan-proven normal brain volume. All the children underwent digital electroencephalography with brain mapping. Results show that alpha posterior dominant rhythm was present in 88 atrophic children and 44 controls. Beta as posterior dominant rhythm was present in an overwhelming 91.5% of atrophic subjects, with 0.009 p-values. The focused occipital Beta-alpha ratio correlated significantly with brain volume loss presented in diagonal brain fraction. The FOBAR and DAR values of the QEEG showed no significant correlation. This work concludes that QEEG cerebral dysfunctional studies may be etiologically and case dependent from the nature of the brain injury. Also, the focused Beta-alpha ratio of the QEEG is a prospective and potential biomarker of consideration in studying childhood atrophic encephalopathy.