Targeted biopsy using multiparametric magnetic resonance imaging increases the detection rate of clinically significant prostate cancer (csCaP). In this meta-analysis, we compare the diagnostic accuracy of transrectal (TR) vs transperineal (TP) approaches for MRI-guided software fusion biopsy (FB) in the detection of csCaP. A literature search was performed in PubMed, Cochrane and Embase electronic databases up until July 2019 following the preferred reporting items for systematic review and meta-analysis system. The pooled sensitivity and specificity of either approach was evaluated using radical prostatectomy or systematic biopsies with ≥24 biopsy cores to be the reference standard. Fourteen papers with a total of 2002 patients were selected. Seven hundred and sixty-five patients underwent TR FB, while 1,387 underwent TP FB. One hundred and fifty of the patients underwent both TR and TP approaches. Both approaches were similar in terms of sensitivity (TR vs. TP: 0.81 vs 0.80) and specificity (TR vs. TP: 0.99 vs 0.95). In terms of likelihood ratios and diagnostic odds ratio, TR performed better than TP approach. The area under the receiving operator curve for both approaches was similar (0.91 vs 0.88 respectively). However, there was substantial heterogeneity across the studies for both approaches. TP and TR approaches to software-based FB yield similar diagnostic performance for the detection of csCaP. When deciding on the approach, physicians should consider other inherent features of either technique that suit their practice.