Background: To evaluate the value of time-of-flight MR angiography (TOF MRA) for the assessment of extracranial-intracranial (EC-IC) bypass in Moyamoya disease in comparison with computed tomography angiography (CTA). Patients and methods: A consecutive series of 23 patients with Moyamoya disease were analyzed retrospectively. Twenty three patients underwent 25 procedures of extracranial-intracranial bypass. Cranial CTA was performed within one week after the surgery to assess bypass patency. Then TOF MRA was scanned within 24 h after CTA on a 3T MRI system. Using 5-point scales (0 = poor to 4 = excellent), two radiologists rated the image quality and vessel integrity of bypass for three segments (extracranial, trepanation, intracranial). Results: Image quality was high in both CTA and TOF MRA (mean quality score 3.84 ± 0.37 and 3.8 ± 0.41), without statistical difference (p = 0.66). Mean scores of TOF MRA with respect to bypass visualization were higher than CTA in the intracranial segment (p = 0.026). No significant difference of bypass visualization regarding the extracranial and trepanation segments was found between TOF MRA and CTA (p = 0.66 and p = 0.34, respectively). For the trepanation segment, TOF MRA showed pseudo lesions in 2 of all 25 cases. Conclusions: 3T TOF MRA, a non-contrast technique not exposing the patients to radiation, proved to be at least equal to CTA for the assessment of EC-IC bypass, and even superior to CTA with respect to the intracranial segment. In addition, readers should be aware of a potential overestimation showing focal pseudo lesions of the bypass at the trepanation segment in TOF MRA.