Objective To assess the diagnostic accuracy and agreement of CT and MRI in terms of the Bosniak classification version 2019 (BCv2019). Materials and methods A prospective multi-institutional study enrolled 63 patients with 67 complicated cystic renal masses (CRMs) discovered during ultrasound examination. All patients underwent CT and MRI scans and histopathology. Three radiologists independently assessed CRMs using BCv2019 and assigned Bosniak class to each CRM using CT and MRI. The final analysis included 60 histopathologically confirmed CRMs (41 were malignant and 19 were benign). Results Discordance between CT and MRI findings was noticed in 50% (30/60) CRMs when data were analyzed in terms of the Bosniak classes. Of these, 16 (53.3%) were malignant. Based on consensus reviewing, there was no difference in the sensitivity, specificity, and accuracy of the BCv2019 with MRI and BCv2019 with CT (87.8%; 95% CI = 73.8–95.9% versus 75.6%; 95% CI = 59.7–87.6%; p = 0.09, 84.2%; 95% CI = 60.4–96.6% versus 78.9%; 95% CI = 54.4–93.9%; p = 0.5, and 86.7%; 95% CI = 64.0–86.6% versus 76.7%; 95% CI = 75.4–94.1%; p = 0.1, respectively). The number and thickness of septa and the presence of enhanced nodules accounted for the majority of variations in Bosniak classes between CT and MRI. The inter-reader agreement (IRA) was substantial for determining the Bosniak class in CT and MRI (k = 0.66; 95% CI = 0.54–0.76, k = 0.62; 95% CI = 0.50–0.73, respectively). The inter-modality agreement of the BCv219 between CT and MRI was moderate (κ = 0.58). Conclusion In terms of BCv2019, CT and MRI are comparable in the classification of CRMs with no significant difference in diagnostic accuracy and reliability.