Background Pulmonary embolism (PE) is a serious condition and has a clinical dilemma in diagnosis. Computed tomography pulmonary angiography (CTPA) is a gold standard in its diagnosis, but MRI has proven a good role in PE diagnosis. Aim The aim of this work was to evaluate the role of noncontrast magnetic resonance pulmonary angiography (MRPA) imaging in diagnosis of acute PE using CTPA as a gold standard. Patients and methods In total, 25 patients with PE confirmed by CTPA were included in this study. All patients underwent computed tomography angiography and noncontrast MRPA on the same day or within three consecutive days. The results were compared and statistically analyzed. Results The mean age of the study group was 46.4 ± 13.5 years. Females represent 60% (15/25) and males represent 40% (10/25). The per-vessel sensitivity of noncontrast MRPA reached to about 100% with specificity 100% at the level of the main trunk, right and left main pulmonary arteries down to segmental arteries. The sensitivity for right subsegmental branches was 25% and left subsegmental branches was 33.3%. Conclusion The noncontrast MRPA has a reasonable sensitivity and specificity in the diagnosis of PE, especially in major branches. So, it can be used as an alternative to the computed tomography angiography, especially when the computed tomography angiography and the use of gadolinium are contraindicated.