Background: Children with nephrolithiasis constitute a high-risk patient population with increased risk for stone recurrence during their life- times, so proper evaluation and management is very important. The present study aimed to compare operative time, complications rate, stone free rate in the prone position versus flank-free modified Supine position (FFMSP) Mini-perc percutaneous nephrolithotripsy (M-PCNL) in pediatric age group. Patients and methods: A prospective randomized comparative study was carried out on 20 patients with renal stones scheduled for PCNL at the Urology Department, Faculty of Medicine, Zagazig University in the period from December 2017 till November 2018, they were randomized in two groups; Group A: for Flank-free Modified Supine position Mini Percutaneous Nephrolithotomy position; Group B: for prone mini percutaneous nephrolithotomy position. Results: the current study showed that there was a statistical significant difference between the studied groups regarding to operative time & position time, it was shorter in FFMS than prone with highly significant difference, also there was no statistical significant difference between the two groups in radiation time, access time and laser time, the needed for auxiliary maneuver as ESWL in both position was 5 cases in both group together, there was no significant difference in studied groups. Conclusion: we conclude that the mini- percutaneous nephrolithotripsy in Flank Free Modified Supine position as treatment of pediatric renal stones is, shorter in operation time, less in complication rate but not significant different and has same efficiency as compared to prone mini-percutaneous nephrolithotripsy.