Preterm birth incidence has increased in recent years and is associated with a rise in long-term neurological and developmental sequelae in children. Because the morbidity and prevalence of developmental deficits increase as the number of weeks of gestation decreases, extremely preterm infants are at greater risk of developing cerebral palsy, severe cognitive impairment, epilepsy, attention/hyperactivity disorders, learning disorders, and autism spectrum disorders. In this study, 15 participants born extremely preterm were followed up from two months until past three years of age. During the first months of postnatal life, the participants received Katona neurohabilitation, which provides vestibular and proprioceptive stimulation through the intensive practice of genetically determined, human-specific elementary movements that present early in life. Subcortical brain volumes from brain magnetic resonance images acquired at the beginning and after the intervention, treatment adherence to Katona neurohabilitation therapy, and neurodevelopmental outcomes were collected. Absolute subcortical volumes increased after treatment, except for pallidum and thalamus. When these subcortical volumes were divided by the total intracranial volume, most volumes decreased, except those for the right amygdala and both hippocampi. The inhibition of subcortical function that results in cortical control and increased connectivity may explain these decreases. The regression analyses showed that after-treatment hippocampal volumes had a discrete predictive value. However, treatment adherence showed a clear association as a predictor of mental and psychomotor neurodevelopment after treatment. Thus, treatment adherence constitutes a relevant factor for the Katona neurohabilitation effectivity.