In prostate cancer with biochemical failure after therapy, current imaging techniques have a low detection rate at the prostate-specific antigen (PSA) levels at which targeted salvage therapy is effective. ¹¹C-choline and ¹⁸F-fluoromethylcholine, though widely used, have poor sensitivity at low PSA levels. ⁶⁸Ga-PSMA (Glu-NH-CO-NH-Lys-(Ahx)-[⁶⁸Ga-N,N′-bis[2-hydroxy-5-(carboxyethyl)benzyl]ethylenediamine-N,N′-diacetic acid]) has shown promising results in retrospective trials. Our aim was to prospectively compare the detection rates of ⁶⁸Ga-PSMA versus ¹⁸F-fluoromethylcholine PET/CT in men who were initially managed with radical prostatectomy, radiation treatment, or both and were being considered for targeted therapy. A sample of men with a rising PSA level after treatment, eligible for targeted treatment, was prospectively included. Patients on systemic treatment were excluded. ⁶⁸Ga-PSMA, ¹⁸F-fluoromethylcholine PET/CT, and diagnostic CT were performed sequentially on all patients between January and April 2015, and the images were assessed by masked, experienced interpreters. The findings and their impact on management were documented, together with the results of histologic follow-up when feasible. In total, 38 patients were enrolled. Of these, 34 (89%) had undergone radical prostatectomy and 4 (11%) had undergone radiation treatment. Twelve (32%) had undergone salvage radiation treatment after primary radical prostatectomy. The mean PSA level was 1.74 ± 2.54 ng/mL. The scan results were positive in 26 patients (68%) and negative with both tracers in 12 patients (32%). Of the 26 positive scans, 14 (54%) were positive with ⁶⁸Ga-PSMA alone, 11 (42%) with both ¹⁸F-fluoromethylcholine and ⁶⁸Ga-PSMA, and only 1 (4%) with ¹⁸F-fluoromethylcholine alone. When PSA was below 0.5 ng/mL, the detection rate was 50% for ⁶⁸Ga-PSMA versus 12.5% for ¹⁸F-fluoromethylcholine. When PSA was 0.5–2.0 ng/mL, the detection rate was 69% for ⁶⁸Ga-PSMA versus 31% for ¹⁸F-fluoromethylcholine, and when PSA was above 2.0, the detection rate was 86% for ⁶⁸Ga-PSMA versus 57% for ¹⁸F-fluoromethylcholine. On lesion-based analysis, ⁶⁸Ga-PSMA detected more lesions than ¹⁸F-fluoromethylcholine (59 vs. 29, P < 0.001). The tumor-to-background ratio in positive scans was higher for ⁶⁸Ga-PSMA than for ¹⁸F-fluoromethylcholine (28.6 for ⁶⁸Ga-PSMA vs. 9.4 for ¹⁸F-fluoromethylcholine, P < 0.001). There was a 63% (24/38 patients) management impact, with 54% (13/24 patients) being due to ⁶⁸Ga-PSMA imaging alone. Histologic follow-up was available for 9 of 38 patients (24%), and 9 of 9 ⁶⁸Ga-PSMA–positive lesions were consistent with prostate cancer (⁶⁸Ga-PSMA was true-positive). The lesion positive on ¹⁸F-fluoromethylcholine imaging and negative on ⁶⁸Ga-PSMA imaging was shown at biopsy to be a false-positive ¹⁸F-fluoromethylcholine finding (⁶⁸Ga-PSMA was true-negative). In patients with biochemical failure and a low PSA level, ⁶⁸Ga-PSMA demonstrated a significantly higher detection rate than ¹⁸F-fluoromethylcholine and a high overall impact on management.