In recent years, multistate outbreaks of Salmonella enterica serovars were traced to tomatoes and resulted in serious economic loss for the tomato industry and decreased consumer confidence in the safety of tomato produce. Purified compounds derived from essential oils such as thymol and carvacrol had wide inhibitory effects against foodborne pathogens including Salmonella. The objective of this study was to determine the antimicrobial activities of thymol, carvacrol, and thyme oil against Salmonella on grape tomatoes. Surface-inoculated grape tomatoes were washed with 4% ethanol, 200 ppm of chlorine, or one of six washing solutions (thymol [0.2 and 0.4 mg/ml], thyme oil [1 and 2 mg/ml], and carvacrol [0.2 and 0.4 mg/ml]) for 5 or 10 min. There was no significant difference in the reduction of S. enterica serovars when different washing times were used (P > 0.05). Thymol (especially at the concentration of 0.4 mg/ml) was the most effective (P < 0.05) among the three natural antimicrobial agents, which achieved >4.1-log reductions of S. enterica serovars Typhimurium, Kentucky, Senftenberg, and Enteritidis on grape tomatoes after a 5-min washing and >4.3-log reductions after a 10-min washing. A >4.6-log reduction in the S. enterica populations in comparison to control was observed with the use of thymol solutions. The uses of these antimicrobial agents achieved significant log reductions of Salmonella on inoculated grape tomatoes and decreased dramatically the risk of potential transmission of pathogens from tomatoes to washing solutions. None of these antimicrobial agents decreased the total phenolic and ascorbic acid content, nor did any of them change the color and pH values or affect the taste, aroma, or visual quality of grape tomatoes. Therefore, 0.4 mg/ml thymol has great potential to be an alternative to chlorine-based washing solution for fresh produce.