The current study was designed to investigate co-occurrence of absolute/relative microcephaly, absolute/relative macrocephaly and congenital nervous system disorders or neurological syndromes with symptoms visible since infancy, based on fundamental data acquired during the admission procedure at a neurological rehabilitation ward for children and adolescents. The study applied a retrospective analysis of data collected during the hospitalization of 327 children and adolescents, aged 4–18 years, affected since infancy by congenital disorders of the nervous system and/or neurological syndromes associated with a minimum of one neurodysfunction. To identify subjects with absolute/relative microcephaly, absolute/relative macrocephaly in the group of children and adolescents, the adopted criteria took into account z-score values for head circumference (z-score hc) and head circumference index (z-score HCI). Dysmorphological (x+/−3s) and traditional (x+/−2s) criteria were adopted to diagnose developmental disorders of head size. Regardless of the adopted criteria, absolute macrocephaly often coexists with state after surgery of lumbar myelomeningocele and hydrocephalus, isolated hydrocephalus, hereditary motor and sensory polyneuropathy, and Becker’s muscular dystrophy (p < 0.001, p = 0.002). Absolute macrocephaly is often associated with neural tube defects and neuromuscular disorders (p = 0.001, p = 0.001). Relative microcephaly often occurs with non-progressive encephalopathy (p = 0.017, p = 0.029). Absolute microcephaly, diagnosed on the basis of traditional criteria, is often associated with epilepsy (p = 0.043). In children and adolescents with congenital nervous system disorders or neurological syndromes with one or more neurodysfunction visible since infancy, there is variation in abnormal head size (statistically significant relationships and clinical implications were established). The definitions used allowed for the differentiation of abnormal head size.