Approximately one percent of the population suffers from schizophrenia, a chronic mental disorder with high heritability, that significantly impacts many aspects of life. The aim of this work was to develop an efficient means of identifying de novo mutations, i.e., new mutations that develop during embryonic development and that are not inherited from parents, in pediatric schizophrenia. To this end, DNA samples from two families, which included a healthy mother, a father and a child with schizophrenia, were exome sequenced. Using two designated algorithms – GATK denovogear and a code written in R language, de novo mutations were identified and ranked according to their probability to be true positives. Following validation, only the mutations that were detected by both algorithms were found to be true positives. These findings demonstrate that the developed approach can efficiently locate mutations and will enable further research and a better understanding of the pathology and biological mechanisms of pediatric schizophrenia.