Objective To investigate the pathogens of ventilator-associated pneumonia (VAP) and their drug resistance in the pediatric intensive care unit (PICU) in high-altitude areas and to provide a clinical basis for the prevention and treatment of VAP. Methods A total of 94 children with VAP hospitalized in the PICU in high-altitude areas between June 2011 and June 2013 were recruited. Their lower respiratory tract secretions were collected for bacterial culture and drug sensitivity test. Results Of the 94 children with VAP, 22 (23%) had a single bacterial infection, and 72 (77%) had mixed infections, mostly with Klebsiella pneumoniae and Acinetobacter baumannii (17 cases, 27%). Of the 178 isolated strains of pathogens, 139 (78%) were Gram-negative bacteria (G^- bacteria), mainly including Klebsiella pneumoniae, Stenotrophomonas maltophilia, Acinetobacter baumannii, and Pseudomonas aeruginosa, 26 (15%) were Gram-positive bacteria (G⁺ bacteria), mainly including Staphylococcus aureus, and 13 (7%) were fungi, mainly including Candida albicans. Most G^- bacteria had a high drug resistance. Pseudomonas aeruginosa was extensively drug-resistant. Acinetobacter baumannii was only highly sensitive to cefoperazone/sulbactam and imipenem. Multidrug resistance (methicillin resistance) was found in G⁺ bacteria, for which vancomycin was effective. Conclusions The pathogens of VAP in high-altitude areas are mostly G^- bacteria, which may cause mixed infections and develop drug resistance. This provides guidance for the rational use of antimicrobial drugs and the development of key prevention and control measures for VAP.