The septum pellucidum is an important thin, membranous structure in the brain that separates the anterior horns of the lateral ventricles, essential for maintaining brain anatomy and function. Here, we describe a case of a 38-year-old male with a 20-year history of seizures, occurring approximately three to four times annually and lasting 30 minutes to one hour per episode, who presented with a recent seizure three days prior. Magnetic resonance imaging (MRI) of the brain revealed an absence of the septum pellucidum in its posterior portion, mild prominence of both lateral ventricles, and an abnormal course of the crura of the fornix, leading to a diagnosis of partial absence of the septum pellucidum. This case underscores the importance of comprehensive neuroimaging in detecting structural brain anomalies, which is crucial for effective diagnosis, management, and improving patient outcomes, particularly in long-standing seizure disorders.