Objective To examine the efficacy and safety (blood?brain barrier permeability) of right hemisphere cerebral perfusion imaging using transcranial ultrasound following skull thinning in the rat. Methods Forty?eight Sprague Dawley rats received local skull?thinning surgery for transcranial ultrasound perfusion imaging (with injection of 0. 15 mL SonoVueTM ). Perfusion findings were compared before and after the skull surgery in six rats, and the brains were examined by magnetic resonance imaging (n = 2) or Evans blue staining (n = 4). The skulls of the rats were also removed for pathological examination to measure the thickness of the remaining skull. Perfusion in the right hemisphere of the brain was analyzed in 48 rats with a time?intensity curve to obtain quantitative transcranial ultrasound perfusion imaging parameters. Results After the surgery, the ultrasound perfusion imaging of the right hemisphere was improved, with typical perfusion patterns including a rapid wash?in and wash?out, and slow clearance of the contrast enhancement. The average peak intensity(PI)value after skull thinning was almost three times higher than that before surgery [(9. 98 ±2. 35) dB vs (3. 24±1. 49) dB, respectively; P < 0. 01], while the time to peak (TTP) was unchanged [(4. 66 ± 0. 45) s vs (3. 86 ±1. 43) s, respectively; P > 0. 01]. The thickness of the thinned skull after grinding was approximately (66.1 ± 11.4)μm. Evans blue staining and magnetic resonance imaging showed no observable blood brain barrier damagses. Conclusions Skull?thinning surgery is safe and can be applied to small animals for quantitative ultrasound imaging without a craniotomy. This minimally invasive and real?time imaging technique may be useful for dynamic studies of cerebral blood flow changes in various animal disease models.