We report the clinical outcomes of mitral valve repair (MVR) in two Boston Terriers with a heart base tumor (HBT). Both dogs had a HBT on the left side of the aortic arch. A right-side approach, which is not a standard MVR procedure in our facility, was considered optimal based on echocardiography and computed tomography images. Case 1 experienced unexpected blood pressure elevation during periaortic tissue dissection to install an aortic root catheter. Aortic clamping was discontinued and MVR was performed under ventricular fibrillation. This dog was unable to recover normal sinus rhythm. Chemodectoma was confirmed by histopathology. Case 2 was able to complete MVR by aortic clamping and it survived for two years following the surgery. Cause of the failure to recover from ventricular fibrillation in Case 1 could not be confirmed, however, a micro air embolism was the most conceivable factor because the aortic cross clamp was not performed. Micro air embolism can be avoided by taking cautious surgical measures, and MVR should be considered as a treatment option in myxomatous mitral valve disease dogs with HBT if prognostic advantages are high enough to achieve a better quality of life.