Both radiolabelled choline and prostate specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) could be used in patients with biochemical recurrent prostate cancer (BRPCa). We aimed to perform a meta-analysis about the head-to-head comparison of detection rate (DR) between these methods in BRPCa. A comprehensive literature search of studies listed in PubMed/MEDLINE, EMBASE and Cochrane library databases through October 2018 and regarding the head-to-head comparison of DR between radiolabelled choline and PSMA PET/CT in BRPCa was carried out. Overall pooled DR was calculated on a per patient-based analysis; subgroup analyses taking into account different prostate-specific antigen (PSA) cut-off values were performed. Five studies (257 BRPCa patients) were included. The meta-analysis provided the following overall DR: 56% [95% confidence interval (95% CI): 37-75%] for radiolabelled choline PET/CT and 78% (95% CI: 70-84%) for radiolabelled PSMA PET/CT. Significant difference of DR was found only in patients with PSA ≤ 1 ng/ml [the DR of radiolabelled choline and PSMA PET/CT were 27% (95% CI: 17-39%) and 54% (95% CI: 43-65%), respectively]. Radiolabelled PSMA PET/CT proved to be clearly superior in detecting BRPCa lesions at low PSA levels (≤ 1 ng/ml) when compared to radiolabelled choline PET/CT. On the other hand, the superiority of radiolabelled PSMA PET/CT was less evident in patients with PSA > 1 ng/ml. More studies and in particular cost-effectiveness analyses comparing these imaging methods are warranted.