Summary This case report describes a 3‐month‐old female Thoroughbred foal that presented following the acute onset of apparent respiratory distress, abnormal head carriage and severe neurological deficits referable to the brainstem or cranial cervical spinal cord. Ultrasonography revealed an abscessing pneumonia. Radiographs did not show evidence of bony pathology at the atlanto‐occipital region, an area consistent with the observed neurological deficits. With magnetic resonance imaging, atlantal and occipital osteomyelitis, atlanto‐occipital septic arthritis, and atlanto‐axial synovitis were diagnosed. Brainstem meningitis and extradural compression were also revealed. Culture of the right occipitoatlantal joint and cerebrospinal fluid yielded a pure culture of Rhodococcus equi. These findings and multifocal R. equi abscessation were confirmed at necropsy.