Introduction: Therapy of choice for symptomatic vascular malformations consists of surgery, sclerotherapy, or embolization. However, these techniques are invasive with possible complications and require hospitalization. We present a novel non-invasive technique, i.e., magnetic resonance-guided high-intensity focused ultrasound (MR-HIFU) ablation, for the treatment of a vascular malformation in a patient. This technique applies high-intensity sound waves transcutaneously to the body and is fully non-invasive. MRI guidance is the novel aspect of HIFU treatments and is used for exquisite delineation and localization of the lesion and accurate real-time temperature monitoring during tissue ablation. MR-HIFU is a well-established treatment option for uterine fibroids and is currently being investigated for, e.g., bone tumors, breast cancer, prostate cancer, and liver cancer. MR-HIFU of vascular malformations has not been a topic of research yet. Case description: Volumetric MR-HIFU ablation of a vascular malformation in the lower extremity of an 18-year-old male patient was performed. Temperatures of 62-80 °C were reached in the target lesion with sonications of 4 × 4 × 8 mm using powers of 200 W for <20 s. At 1-month follow-up, the patient reported qualitatively sustained reduction of pain and normal motor function. Three-month follow-up imaging indicated successful nidus destruction, which resulted in reduction of >30 % of the tumor volume. After 13 months, pain score was reduced to <2 after extreme exertion for several hours and to 0 for daily activities. Discussion and evaluation: Radiofrequency ablation and cryoablation are minimally invasive techniques that have been tried on low-flow vascular malformations with inconsistent results. Furthermore, both techniques require probe insertion, which is associated with risks of wound infection and hospitalization. Since MR-HIFU is truly non-invasive, these risks are negligible. Conclusions: In conclusion, we reported a successful non-invasive treatment of a vascular malformation with MR-HIFU in a clinical patient including long-term follow-up data for the first time. The patient reported qualitatively sustained pain reduction up to 13 months post treatment.