Horseshoe kidney is a rare congenital anomaly resulting from the fusion of the lower pole leading to medial and caudal deviation of kidneys that pose challenges to successful stone clearance. We evaluated the various patient- and treatment-related factors that can impact successful stone clearance. A total of 34 patients with 36 renal moieties with urolithiasis in horseshoe kidneys from 2015 to 2021 were included with a median age of 38 years (11–56 years). The mean calculus size was 39.27 mm (21–70 mm). Twenty-two patients had left, 10 had right, and 2 had bilateral disease. Twelve patients (33%) had previous interventions done. As per Guy stone score (GSS), 14 patients had grade IV, 16 patients had grade III, and 4 patients had grade II disease. Of these patients, 22 underwent unilateral percutaneous nephrolithotomy (PCNL), 2 underwent bilateral PCNL, 6 had pyelolithotomy, 2 had right nephrectomy, and 2 patients underwent shockwave lithotripsy (SWL). Six patients undergoing pyelolithotomy had complete clearance. In PCNL, infra-costal puncture was done uniformly. Complete clearance was seen in 12 out of 16 with superior calyceal access (75% stone-free rates, SFR), 2 out of 8 with middle calyceal puncture (25% SFR), and both the cases with inferior calyceal puncture (100% SFR). Factors affecting stone clearance are as follows: GSS, i.e., grade < IV vs ≥ IV (71.4 vs 50%, P = 0.42), STONE score < 12 vs ≥ 12 (83.3 vs 28.5%, P = 0.048), stone size < 40 vs ≥ 40 mm (50 vs 71.4%, P = 0.42). Our analysis showed that stone clearance was independent of mode of access, GSS, or stone size, although STONE score was a predictor of successful outcomes in PCNL. [ABSTRACT FROM AUTHOR]