Checkpoint inhibitor immunotherapy has recently been proven to be an attractive treatment option for a wide variety of malignancies. Nivolumab, an anti-programmed cell death protein-1 antibody, has been proven effective and safe in treating metastatic renal cell carcinoma (RCC) with a clear cell component. We report the case of a patient with high-grade clear cell RCC with rhabdoid features who has achieved a durable complete response with nivolumab therapy after multiple surgical interventions and progression on pazopanib. Genomic evaluation in this case was characterized in part by a PBRM1 variant, similar to the only other described case of RCC with rhabdoid features obtaining a complete response to nivolumab. This case supports the potential utility of checkpoint inhibitors in aggressive, rare subtypes of RCC where there are limited options for therapy.