Although congenital ureteropelvic junction (UPJ) obstruction is the most common cause of neonatal hydronephrosis, aetiopathogenesis is still inconclusive. Recently, the paucity of interstitial cells of Cajal (ICC) at the narrow adynamic part of UPJ has been implicated as a causative factor. This prospective study was conducted between October 2019 and March 2022 to find out the density of ICC by the immunohistochemical method using CD117 (c-kit) antibody, in resected segments of UPJ in obstruction patients and in renal tumour patients as control. ICC/high power field (hpf) was also studied from the margins of the resected segment in the obstruction group. The pre-operative and post-operative sonographic and renal scintigraphic features were compared. The median age of patients in the study group (n = 25) was 36 months and in the control group was 39 months. The mean ICC/hpf at the stenotic part of UPJ in the study group was 3.56 ± 1.26 and in the control group was 12.56 ± 1.89 (P = 0.0001). ICC density from the proximal and distal margins of the resected segment was 11.12 ± 2.12 and 11.68 ± 1.62, respectively (P < 0.001). The post-operative antero-posterior diameter of the renal pelvis and differential renal function showed significant improvement in comparison to the pre-operative value (P = 0.0045 and 0.0005, respectively). The significant decrease in the density of ICC at the stenotic part of UPJ compared to controls suggests a pacemaker role of these cells in ureteral peristalsis and the aetiopathogenesis of UPJ obstruction. Histopathological analysis of ICC should not only be limited to the stenotic part of UPJ but also should focus on the anastomosed ends of the ureter, which reflects post-pyeloplasty outcome.