Context: Pediatric diarrhea is often associated with dysbiosis and pathogenic microorganisms, necessitating further molecular investigation. Differential gene expression (DEG) analysis offers potential insights into biomarkers for the molecular pathogenic mechanisms of diarrhea and antibiotic resistance in children. Aims: To identify differentially expressed genes (DEGs) associated with pathogenicity and antimicrobial resistance by analyzing publicly available transcriptomic two datasets (GSE69529 and GSE54070) in children with diarrhea. Methods: DEG analysis was performed using GEO2R on GSE69529 and GSE54070 datasets. Multiple machine learning models (SVM, RF, NN, LR, XGBoost) were applied via Orange 3.10.2 for cross-validation. Cytoscape and databases such as STRINGdb, IntAct, and CTD were utilized for protein interaction and upstream regulatory analysis. To confirm ARGs, five fecal cohort samples were collected from the primary public health in Jakarta, Indonesia, and analysed using the Vitek-2 compact system. Results: Key DEGs included RYK, CREBL2, and ST14, associated with intestinal integrity, inflammation, and immune regulation. Seven resistance genes were commonly identified in different age groups. Pathogen mapping revealed Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, and Salmonella typhimurium as dominant. Resistance-related genes such as mexA/acrA, arnA, tolC, and mexB/acrB were implicated in β-lactam and CAMP resistance pathways. Resistance genes common to different age groups included tetO, tetQ, and SUL2. To validate those findings, Support Vector Machines and Neural Networks exhibited the best classification performance for machine learning models. Conclusions: Several genes identified among DEGs related to pathogenicity and antimicrobial resistance markers may serve as potential biomarkers for developing diagnostic and therapeutic targets for pediatric diarrhea. © (2026), (Academic Association of Pharmaceutical Sciences from Antofagasta (ASOCIFA)). All rights reserved.