Identification of a single epileptogenic focus in patients with tuberous sclerosis complex is a challenge. Noninvasive imaging modalities, including subtraction ictal single-photon emission computed tomography coregistered to magnetic resonance imaging (SISCOM), have been used to determine the dominant epileptogenic focus for surgical resection. We assessed whether complete resection of SISCOM hyperperfusion abnormality correlates with seizure-free outcome in 6 children with tuberous sclerosis complex-related epilepsy. The median seizure onset age was 4 months (range 1 day to 16 months). The age at surgery ranged from 8 months to 13 years. A dominant SISCOM hyperperfusion focus was identified in 5 patients with multiple tubers. SISCOM provided additional localizing information for epilepsy surgery in 3 patients with nonlocalizing or discordant electrophysiologic and neuroimaging findings. At a minimum of 2 years’ follow-up, 3 patients were free of seizures overall. Freedom from seizures was associated with complete resection of SISCOM abnormality in 2 patients. These findings demonstrate that SISCOM can be useful in identifying the epileptogenic zone and in guiding the location and extent of epilepsy surgery in children with tuberous sclerosis complex and multifocal abnormalities. In children with tuberous sclerosis complex and intractable epilepsy, complete resection of the SISCOM hyperperfusion abnormality is associated with freedom from seizures.