To investigate the comparative diagnostic accuracy of cardiac computed tomography (CT) and transoesophageal echocardiography (TEE) for detecting infective endocarditis. Original publications published in English language before July, 2021 were thoroughly search in PubMed, CENTRAL (Cochrane Central Register of Controlled Trials), and Google Scholar literature databases. Studies were included if they used CT and/or TEE as an index test, presented data on valvular complications related to infective endocarditis, and used surgical findings as to the reference standard. Literature screening identified fifteen studies that fulfilled the inclusion criteria. Meta-analysis showed that CT sensitivity for detecting valvular abscesses was higher than that of TEE [0.88 (95% confidence interval [CI]: 0.82 to 0.94; 11 studies involving 842 subjects) versus 0.74 (95%CI: 0.65 to 0.84) P = 0.015; 12 studies involving 917 subjects]. TEE showed statistically significantly greater sensitivity than CT for detecting valvular vegetation [0.91 (95% CI: 0.84 to 0.97, 11 studies involving 971 subjects) versus 0.80 (95% CI: 0.69 to 0.82), 12 studies involving 915 subjects, P =0.019. In case of leaflet detection, TEE showed statistically significantly higher sensitivity than CT (0.76 vs 0.46, P =0.010). CT performs statistically significantly better than TEE for detecting abscesses while TEE provides statistically significant superior results for detecting vegetation. There is a need for well-designed prospective studies to further corroborate these findings.