The impact of energy flux density (EFD) used on low-intensity shockwave therapy (LiST) for erectile dysfunction (ED) has not been explored. Our aim was to compare EFD 0.05 versus 0.10 mJ/mm2 regarding efficacy and safety of 12-treatment sessions when applied two or three times per week. Ninety-seven patients with vasculogenic ED, PDE5 inhibitors users were randomized into four groups, to receive 12 LiST sessions. Group A (n = 24) : two sessions per week, EFD 0.05 mJ/mm2; Group B (n = 24): three sessions per week, EFD 0.05 mJ/mm2; Group C (n = 24): two sessions per week, EFD 0.10 mJ/mm2; Group D (n = 25): three sessions per week, EFD 0.10 mJ/mm2. International Index for Erectile Function-Erectile Function domain (IIEF-EF), Minimally clinical important differences (MCID), sexual encounter profile, and triplex ultrasonography parameters were used to asses erectile function. Eighty-nine patients completed the 6-month follow-up (FU). All four groups improved in mean IIEF-EF score, average SEP3 "Yes" response rates at 6-month FU visit compared with baseline (p < 0.001). MCID at 6-month FU visit was achieved in 82.6%, 77.3%, 87%, and 81% in Groups A, B, C, and D, respectively. Mean PSV (cm/s) at baseline versus 3-month FU visit were 30.32 versus 34.67 for Group A, 30.02 versus 35.02 for Group B, 30.2 versus 36.02, for Group C, 29.43 versus 34.3 for Group D (p < 0.01). There were no statistical significant differences in the change of all outcome measures assessing erectile function between different sessions frequency. A tendency for better efficacy using EFD 0.10 mJ/mm2 was noticed, although it did not reach statistical significance. No treatment-related side-effects were reported. This study lacks a sham-controlled arm. However, all patients were randomized to the four groups, and baseline characteristics were similar between the groups. Moreover, arterial insufficiency was confirmed among all patients by penile triplex ultrasonography. Conclusively, patients may benefit equally when sessions are applied either two or three per week. An EFD of 0.10 mJ/mm2 could result in better outcomes, but further studies are needed to validate this observation.