High intensity focused ultrasound (HIFU) mechanical ablation is an emerging technique for non-invasive transcranial surgery. Lesions are created by driving inertial cavitation in tissue, which requires significantly less peak pressure and time-averaged power compared with traditional thermal ablation. The utility of mechanical ablation could be extended to the brain provided the pressure threshold for inertial cavitation can be reduced. In this study, the utility of perfluorobutane (PFB)-based phase-shift nanoemulsions (PSNEs) for lowering the inertial cavitation threshold and enabling focal mechanical ablation in the brain was investigated. We successfully achieved vaporization of PFB-based PSNEs at 1.8 MPa with a 740 kHz focused transducer with a pulsed sonication protocol (duty cycle = 1.5%, 10 min sonication) within intact CD-1 mice brains. Evidence is provided showing that a single bolus injection of PSNEs could be used to initiate and sustain inertial cavitation in cerebrovasculature for at least 10 min. Histologic analysis of brain slices after HIFU exposure revealed ischemic and hemorrhagic lesions with dimensions that were comparable to the focal zone of the transducer. These results suggest that PFB-based PSNEs may be used to significantly reduce the inertial cavitation threshold in the cerebrovasculature and, when combined with transcranial focused ultrasound, enable focal intracranial mechanical ablation.