Background: Burkholderia cepacia complex (BCC) is known for its resistance to antibiotics and sporadic occurrence in various infections, including bloodstream infections. Its association with neurological disorders, such as Rasmussen Encephalitis (RE), remains poorly understood. Case presentation: We describe a 4-year-old girl with RE and Super Refractory Status Epilepticus, a condition characterized by frequent seizures that do not respond to conventional treatments. Despite initial treatment, her condition worsened, and blood cultures revealed the presence of Burkholderia species. Adjusting the antibiotic therapy to target this specific pathogen led to significant improvement in her clinical status. Conclusion: Our case highlights the rare occurrence of BCC bloodstream infection in a child with complex neurological issues. Although the precise link between BCC and neurological disorders is unclear, our findings contribute to the growing body of evidence that BCC can cause severe infections beyond the respiratory system. This case underscores the importance of accurate diagnosis and tailored treatment in managing such challenging infections effectively.