Introduction Percutaneous nephrolithotomy (PNL) is the treatment of choice in children with complex and large stones. With the experience gained from adult practice, supine PNL is increasingly performed in children as well. We aimed to evaluate the comparative results of prone and supine mini-PNL (m-PNL) performed for large/complex stones in children. Patients and methods The study included children who underwent supine and prone m-PNL at two centers between September 2019-2022. Patients were divided into two groups with a 1:1 ratio to index supine m-PNL and prone m-PNL cases for the size, number, location of the stones, degree of hydronephrosis and age. Operative related parameters, success and complication rates are being discussed on a procedure based manner. Results Fourty-two patients (21 supine, 21 prone) were included. The mean age was 9,6±4 years, mean stone size was 28,8±13,6 mm. Regarding the operative data, while the mean duration of procedure time was 65,7±17,8 min in supine group, 86,9±19,0 min in prone group (p=0,001). Fluoroscopy time was shorter in supine group (p=0,027). While tubeless PNL was performed in 11 cases of prone group (52%) , this number was 18 (86,7%) in supine group (p=0,019). Stone-free rates were similar in both groups (supine m-PNL:90,5%, prone m-PNL:85,7%, p=0.634). Complications were minor in nature in the majority of the cases of both groups which resolved with supportive measures in a short period of time. However, there was a statistically significant difference regarding the location and number accesses between two groups (p=0,008). Simultaneous flexible URS was performed in 8 patients in the supine PNL group (<0,001). Conclusions Our current findings and the highly limited data reported in the literature indicate that as an established minimal invasive treatment alternative m-PNL procedure in supine position can also be performed with similar success and complication rates in pediatric population.