Objectives To compare the diagnostic efficiency of whole-body MRI-DWI and PET/CT in lymphoma staging. Methods A prospective study enrolled 92 patients with lymphoma. Prior to treatment, all patients underwent whole-body MRI-DWI and PET-CT. The methods' efficiency was compared in the diagnosis of lymph node (LN) and organ involvement, and in determining lymphoma stage. Results Sensitivity, specificity, and accuracy in the diagnosis of enlarged LN involvement were 98.2%, 99.9%, and 99.3%, respectively, for MRI-DWI, and 99.4%, 100.0%, and 99.8%, respectively, for PET/CT. ROC analysis showed similar methods' efficiency in the diagnosis of enlarged LN involvement (p > 0.06). MRI-DWI and PET/CT sensitivity in the diagnosis of non-enlarged LN involvement was 77.8% and 88.1%, respectively (p < 0.001). MRI-DWI and PET/CT sensitivity, specificity, and accuracy in the diagnosis of lung involvement were 73.3%, 98.7%, 94.6% and 86.7%, 98.7%, 96.7%; spleen involvement 54.8%, 98.3%, 83.3% and 100.0%, 100.0%, 100.0%; bone marrow involvement 87.1%, 96.4%, 93.0% and 64.5%, 87.3%, 79.1%; and all-organ involvement 72.9%, 98.1%, 91.4% and 80.0%, 96.6%, 92.2%, respectively. ROC analysis showed similar methods' efficiency in the diagnosis of lung involvement (p > 0.3), higher for PET/CT in spleen involvement (p < 0.0001), higher for MRI-DWI in bone marrow involvement (p < 0.0008), and similar in all-organ involvement (p > 0.35). MRI-DWI and PET/CT determined the correct lymphoma stage in 79 (86%) patients. Conclusions Whole-body MRI-DWI and PET/CT determined the correct lymphoma stage in similar numbers of patients. MRI-DWI can serve as a non-irradiative alternative to PET/CT in lymphoma staging.