Nowadays, there is still no consensus on the most accurate PET radiopharmaceutical to early detect prostate cancer (PCa) relapse. A tailored radiotracer choice based on a specific patient’s profile could ensure prompt disease detection and an improvement in patients management. We aimed to compare the [
18F]fluciclovine and [
18F]fluorocholine PET/CT detection rate (DR) in PCa patients restaged for early biochemical recurrence (BCR), according to clinical and biochemical features. A cohort of 138 PCa patients with early BCR (mean age: 71 y, range: 50–87 y) were homogeneously randomized 1:1 to a [
18F]fluciclovine or a [
18F]fluorocholine PET/CT group. The respective PET/CT DR, according to per-patient and per-region analysis, and the impact of the biochemical, clinical, and histological parameters, were compared. The PSA cut-off values predictive of a positive scan were also calculated. Overall, the [
18F]fluciclovine PET/CT DR was 64%, significantly higher than the [
18F]fluorocholine PET/CT DR of 35% (
p = 0.001). Similarly, in the per-region analysis, the [
18F]fluciclovine PET/CT DR was 51% in the prostate region, significantly higher compared to 15% of [
18F]fluorocholine (
p < 0.0001). Furthermore, a statistically significant higher DR in per-patient and per-region (prostate/prostate bed) analysis was observed in the [
18F]fluciclovine group for 0.5–1 ng/mL (
p = 0.018,
p = 0.049) and >1 ng/mL (
p = 0.040,
p < 0.0001) PSA values. A PSA of 0.45 ng/mL for [
18F]fluciclovine and of 0.94 ng/mL for [
18F]fluorocholine was identified as the optimal cut-off value in predicting a positive PET/CT scan. Our results demonstrated a better [
18F]fluciclovine PET/CT DR compared to [
18F]fluorocholine for restaging PCa patients in early BCR, particularly in the detection of locoregional recurrence. The significantly higher [
18F]fluciclovine DR for low PSA values (PSA < 1 ng/mL) supports its use in this setting of patients.
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