To compare the long-term effectiveness, complications, and outcomes of primary obstructive megaureter (POM) treated by endoscopic balloon dilation under fluoroscopic guidance versus not using radioscopy during the procedure. A comparative study between POM cases treated at our institution by endoscopic balloon dilation (EBD) under fluoroscopic guidance (FG) (n = 43) vs no fluoroscopic guidance (NFG) (n = 48) between the years 2004 and 2018 was conducted. The procedure in FG consisted of performing a retrograde pyelography before dilation.Then, a guidewire is introduced to the renal pelvis, and the dilation of the vesicoureteral junction is performed using high-pressure balloon catheters under fluoroscopic vision. Finally, a double-J stent is placed between the renal pelvis and bladder. The procedure in NFG was performed exclusively under cystoscopic vision without radiological exposure. Complications, outcomes, and success rates were analyzed using Spearman's correlation test. Mean follow-up was 12.5 ± 2.2years in FG and 6.4 ± 1.3years in NFG. MAG-3 showed significant differences in renal drainage before and after endoscopic treatment in both groups (p < 0.001 T-test). Statistical analysis did not reveal differences between groups in initial technical failure (r: - 0.035,p = 0.74), early postoperative complications (r: - 0.029,p = 0.79), secondary VUR (r: 0.033, p = 0.76), re-stenosis (r: 0.022, p = 0.84), long-term ureteral reimplantation (r: 0.065, p = 0.55), and final outcome (r: - 0.054, p = 0.61). The endoscopic approach of POM had a long-term success rate of 86.5% in FG VS 89.6% in NFG. Endoscopic balloon dilation of POM can be done with no radiation exposure with similar results, effectiveness, and outcomes.