Purpose: Colonoscopy is considered the most reliable method for the diagnosis of juvenile polyps. However, colonoscopic screening is an invasive and expensive procedure. Fecal calprotectin (FCP), a marker of intestinal inflammation, has been shown to be elevated in patients with polyps. Therefore, this study aimed to evaluate FCP as a screening biomarker for the diagnosis of juvenile polyps. Methods: This cross-sectional, observational study was conducted at the Pediatric Gastroenterology and Nutrition Department, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh. For children with polyps, colonoscopic polypectomy and histopathology were performed. FCP levels were analyzed before and 4 weeks after polypectomy in all patients. Information was recorded in a datasheet and analyzed using the computer-based program SPSS. Results: The age of the children was between 2.5 and 12 years. Approximately 93% of the polyps were found in the rectosigmoid region. Children with juvenile polyps had elevated levels of FCP before polypectomy that subsequently normalized after polypectomy. The mean FCP levels before and after polypectomy were 277±247 µg/g (range, 80–1,000 µg/g) and 48.57±38.23 µg/g (range, 29–140 µg/g) (p<0.001), respectively. The FCP levels were significantly higher in patients with multiple polyps than in those with single polyps. Moreover, mean FCP levels in patients with single and multiple polyps were 207.6±172.4 µg/ g and 515.4±320.5 µg/g (p<0.001), respectively. Conclusion Colonic juvenile polyps were found to be associated with elevated levels of FCP that normalized after polypectomy. Therefore, FCP may be recommended as a noninvasive screening biomarker for diagnosis of colonic juvenile polyps.