Burkholderia cepacia is an aerobic opportunistic Gram-negative pathogen that mainly infects immunodeficiency patients. However, soft tissue infections with fractures due to Burkholderia cepacia are rare with no cases reported. Here, we report a rare case of 3 years of brain death in a 43-year-old woman with Burkholderia cepacia resulting in an occipital subcutaneous abscess and fracture. Through the second-generation sequencing of the whole genome of this strain, it was found that there were no high virulence genes and virulence factors. The patient received targeted antibiotic therapy and showed improvement in clinical symptoms and radiological signs. Bone destruction because of Burkholderia cepacia is easily overlooked due to the lack of characteristic symptoms and limited clinical examination. This case reminds us that Burkholderia cepacia without major virulence factors could damage the bone in immune-compromised patients.