Purpose Previously, we reported elevated level of urine carbohydrate antigen 19-9 (CA 19-9) in childern with ureteropelvic junction obstruction (UPJO). In present study we aimed to investigate the role of urinary CA 19-9 as a predictive biomarker to serve as a surrogate in differentiating between children with UPJO in need of pyeloplasty and those with dilated nonobstructed kidneys suitable for conservative treatment. Material and Methods The study included 36 children with UPJO treated with pyeloplasty (GI) and 24 children with dilated nonobstructed kidneys who were treated conservatively (GII). Voided urine samples were obtained for CA 19-9 measurement before treatment, and every 3 months during follow-up. Additionally, ultrasonography in three-month intervals and annual renography were performed. Follow-up ranged from 12-27 months (average 16.4 months). pyeloplasty was considered for patients with >10% loss of renal function. Results In GI preoperative CA 19-9 was significantly higher than in GII and a cutoff value of 41.06 U/ml yielded a sensitivity of 96.7% and a specificity of 93%. Compared to initial measurements, CA 19-9 decreased significantly at 3 months after pyeloplasty in GI and in the 12th month in GII with significant correlation with changes in renal pelvis diameter. In three patients due to rising CA 19-9 levels during follow-up along with decline in renal function (mean 12.8%) pyeloplasty was considered. Conclusions Urinary CA 19-9 is a non-invasive clinically applicable marker for definition of management protocol in children with UPJO. The practical clinical implications of the biomarker for long-term follow-up of children with UPJO after pyeloplasty and those receiving conservative treatment are significant.