The 2009 pandemic influenza A (H1N1) has been recognized to cause neurological complications including seizures and encephalopathy. We identified 18 children with 2009 H1N1 influenza and neurological complications from first and second wave activity, and compared characteristics to seasonal influenza. Seizures, encephalopathy, and status epilepticus were common presentations. Focal neurological symptoms persisted in 22% of patients at discharge. Compared to seasonal influenza, patients with pandemic 2009 influenza were more likely to have encephalopathy, focal neurological findings, aphasia, and abnormal electroencephalographic findings. In addition, we noted a trend toward heightened neurological complications following second wave influenza activity.