To investigate the efficacy, tolerability, and patient's preference of alprostadil cream for topical use administered within the urethral meatus versus the standard administration route, in erectile dysfunction (ED) treatment. Seventy-one patients (mean age 59.7 ± 9.0 years) affected by ED were analyzed in this multicenter, randomized, two-administration routes, cross-over trial. All patients received a single dose of alprostadil cream applying the dispenser to the tip of the penis (without contacting the urethral meatus) (Standard administration route or ST.AR) alternating with a single dose of alprostadil cream applying the dispenser within the urethral meatus (New administration route or NEW.AR) separated by a one-week washout period, according to randomization. The primary objective of the study was to evaluate the change in International Index of Erectile Function (IIEF-5) total score from baseline to the control visit by comparing the ST.AR and NEW.AR. Secondary objectives of the study were to compare the different methods of administration by evaluating the change in the Sexual Encounter Profile (SEP-2 and SEP-3) questionnaire score and the Patient Reported Outcomes (PROs) by scoring the Patient Self-Assessment of Erection (PSAE) questionnaire. The treatment safety profile was assessed by analysis of adverse events (AEs). Based on the study findings it is evident that the NEW.AR is more efficacious than the ST.AR in improving IIEF-5 and SEP scores from baseline to control visit (IIEF-5: +3.8 vs +6.3; p < 0.001; positive response to SEP-2: 10 vs 27; p = 0.002) and in terms of PSAE (a significant improvement from the baseline in 31% of patients; p < 0.001). As regards the safety profile, no difference in terms of local and systemic side effects was found.