Although many ureteral stents are commercially available, the actuality of encrustation is yet to be elucidated in humans. This study compared the Tria Ureteral Stent with PercuShield and the Polaris Ultra Ureteral Stent with HydroPlus Coating for short-term encrustation formation. Eighty-four patients, who required ureteral stent placement after ureteroscopy, were randomized into two stent groups. After stent removal on postoperative day 14, the encrustation volume on the stent surface was measured by micro-computed tomography. The primary outcome was the inner luminal encrustation volume. Secondary outcomes were encrustation volume on the outer or total surfaces and occurrence of adverse events. Clinical factors related to encrustation were also assessed as a post-hoc analysis. Finally, of the 82 patients analyzed, 75 (91.5%) had encrustation in the inner lumen of the stent. The difference in median inner encrustation volume between the Tria and Polaris Ultra stents was comparable (0.56 vs. 0.37 mm3, P = 0.183). There was no difference observed in the encrustation volume on the outer/total surfaces and stent-related adverse events. In both ureteral stents, the shaft body showed significant inner luminal encrustation compared to the proximal or distal loop (all, P < 0.05). Dyslipidemia (P = 0.027), elevated urine pH (P = 0.046), and crystalluria (P = 0.010) were associated with encrustation formation. The Tria and Polaris Ultra stents had similar efficacy for preventing encrustation in the short-term. Further studies are required to compare their long-term patency.