Premature ejaculation (PE) is the most common male sexual dysfunction. Selective serotonin reuptake inhibitors (SSRIs) are currently recommended for PE. However, the side effects of SSRIs, such as nausea, vomiting, and xerostomia, pose challenges to clinicians. Simultaneously, evidence indicates that psychological and behavioral treatments are often insufficient. LibidUp-PE is a nutraceutical designed to enhance sexual wellness and contains a combination of essential amino acids to boost stamina and vigor, addressing concerns like erectile dysfunction (ED). This study aimed to assess the safety and efficacy of LibidUp-PE in the treatment of PE. In this crossover, double-blind, placebo-controlled trial, 76 patients with PE were randomly divided into two groups. Group A received LibidUp-PE, whereas Group B received a placebo for 12 weeks. Following a 2-week wash-out period, the groups switched treatments for another 12 weeks. Intravaginal ejaculatory latency time (IELT) and post-ejaculatory refractory time (PERT) were measured as the primary outcomes to evaluate PE improvement. Plasma serotonin levels were measured as secondary parameters using enzyme-linked immunosorbent assay. The results showed that LibidUp-PE significantly improved the IELT score, increasing from 0.8 ± 0.2 min to 2.9 ± 1.1 min (p < 0.01). PERT scores also significantly decreased from 15.8 ± 1.7 min to 5.6 ± 0.6 min after 12 weeks of LibidUp-PE treatment. Plasma serotonin levels significant increased from 93.6 ± 7.8 ng/mL to 168.4 ± 12.8 ng/mL (p < 0.001) with LibidUp-PE treatment. In contrast, no significant improvements were observed in the placebo group. Notably, none of the participants withdrew their consent due to adverse reactions, which is indicative of the safety and tolerability of LibidUp-PE. In conclusion, 12-week treatment with LibidUp-PE demonstrated a beneficial effect in reducing PE symptoms, as reflected by improved IELT, reduced PERT, and increased plasma serotonin levels. Therefore, LibidUp-PE could be a promising solution for individuals with PE.