Objectives: To investigate whether PET/CT or PET/MRI is more appropriate for imaging prostate cancer, in terms of for primary tumor detection, local staging and recurrence, as well as lymph nodes and distant metastases. Methods: A systematic literature search was conducted on Embase, PubMed/MEDLINE, and the Cochrane Library database. Studies evaluating the diagnostic performance of PET/CT vs PET/MRI in prostate cancer patients were emphasized. Results: We reviewed 57 original research articles during the period 2016—2021: 14 articles regarding the radiotracer PSMA; 18 articles regarding the primary tumor detection, local tumor staging, managing local recurrence; 17 articles for managing lymph node metastases; and eight articles for managing bone and other distant metastases. PSMA PET could be complementary to mpMRI for primary prostate cancer localization and is particularly valuable for PI-RADS three lesions. PET/MRI is better than PET/CT in local tumor staging due to its specific benefit in predicting extracapsular extension in MRI-occult prostate cancer patients. PET/MRI is likely superior as compared with PET/CT in detecting local recurrence, and have slightly higher detection rates than PET/CT in lymph node recurrence. PET/CT and PET/MRI seem to have equivalent performance in detecting distant bony or visceral metastases. Conclusion: In conclusion, PET/MRI is suitable for local and regional disease, either primary staging or restaging whereas PET/CT is valuable for managing distant bony or visceral metastasis. Advances in knowledge: We reviewed the emerging applications of PET/MRI and PET/CT in clinical aspects. Readers will gain an objective overview on the strength and shortfalls of PET/MRI or PET/CT in the management of prostate cancer.