Purpose: In children with Langerhans Cell Histiocytosis (LCH), FDG-PET/CT is used for staging and response assessment. Whole-body MRI (WB-MRI) can serve as an ionizing radiation-free alternative for repeated whole-body imaging. The aim of this study was to compare WB-MRI with FDG-PET/CT for staging and response assessment in pediatric LCH. Methods: This was a prospective cohort study conducted at an apex tertiary care center from August 2021 to March 2023 after approval from the Institutional Ethics Committee. WB-MRI was done in biopsy-proven cases of LCH, 18 years old or less, undergoing FDG-PET/CT for staging or response assessment. With FDG-PET/CT as the reference standard, diagnostic accuracy and agreement for stage and response assessment were calculated. Assessment of impact on clinical management and image quality was done. Results: Eleven patients of LCH (F:M=5:6, mean age: 6.95 y) were included. Diagnostic accuracy and agreement were 90.6% and 80% (kappa: 0.69) at baseline; 96% and 83.3% (kappa: 0.74) at follow-up, respectively. Clinical management was altered in 2 of 11 patients based on WB-MRI. Image quality was rated as 3.91 +/−1.30 and 4.82 +/− 0.40; artifacts 3.82 +/− 1.33 and 4.55 +/− 0.52 in 11 scans for DWI and STIR, respectively (1 worst, 5 best). Conclusion: Diagnostic accuracy and absolute agreement of WB-MRI were high at baseline and follow-up in LCH. WB-MRI can provide a radiation-free alternative to FDG-PET/CT in children with LCH.