A boy with shaken baby syndrome first presented at age 3 months with acute subdural hematoma (SDH) and was treated by subdural tapping at a local hospital. Chronic SDH was identified at a rehabilitation center at age 19 months. The chronic SDH appeared to have developed within the preceding 16 months. His physical and mental development was already delayed. Magnetic resonance (MR) imaging revealed a 20-mm thick right chronic SDH with midline shift and small bilateral subdural effusions. The chronic SDH had compressed the right cerebral hemisphere. MR imaging also disclosed bilateral cerebral atrophy. 99mTc-ethylcysteinate dimer single photon emission computed tomography (SPECT) revealed decreased cerebral blood flow (CBF) in the non-hematoma hemisphere, although CBF is said to decrease on the chronic SDH side, especially if midline shift is present. Burr hole craniotomy with external drainage was performed, but the patient showed no change in CBF postoperatively, although the volume of hematoma decreased. The patient was clinically unchanged immediately after the operation. In this case, SPECT measurement of CBF was important in evaluating the pathophysiology of the delays in physical and mental growth. Atrophy of the bilateral hemispheres was the major mechanism in the decreased CBF, not the compression by chronic SDH. MR imaging and SPECT can determine the surgical indications for chronic SDH in patients with cortical atrophy.