Background: Acid suppressive medications are used to prevent stress ulcers in critically ill patients. Few studies have been done to evaluate the effect of ranitidine and pantoprazole on stress ulcers. We aimed to compare the effects of ranitidine and pantoprazole on Ventilator Associated Pneumonia (VAP). Materials and Methods: In this double-blind randomized controlled trial, we enrolled 120 traumatic patients with trauma admitted to the intensive care unit (ICU) of Besat Hospital in Hamadan Province located in northwest Iran. The patients were divided into two equal groups receiving either intermittent intravenous ranitidine or pantoprazole to prevent stress ulcers. The incidence of VAP, duration of tracheal intubation, length of ICU stay, duration of hospital stay, and the outcome of treatment including mortality or hospital discharge were compared in both groups. Results: The incidence of VAP was 10% and 30% in patients receiving ranitidine and pantoprazole, respectively (P=0.006). There was no significant difference between the two groups with respect to the duration of tracheal intubation. However, the patients treated with pantoprazole stayed at the hospital two days longer than the other patients (P=0.027). Although patients with VAP stayed at the hospital for 12 more days, the two groups had almost equal mortality rates (P=0.572). Conclusion: ICU patients using pump inhibitors have a three-fold increased risk of developing VAP in comparison to H2-blocker receivers. Thus, prevention of stress ulcers should be limited to its own specific indications.