In this study the anticancer activity of Lavender aqueous extract against MKN45 cell line was evaluated. Plant-based drugs are regarded as promising therapies. Lavender is a plant that has been cultivated from ancient times. An aqueous extract of Lavender has shown therapeutic effects on the nervous system in the high doses based on in-vivo studies. Gastric cancer is one of the frequent cancers in Iranian population. We therefore assessed the effect of Lavender upon a gastric cancer cell line. The MKN45 cancer cell line was selected for treatment with aqueous extract of Lavender. Survival of MKN45 cell line was studied in the presence of various concentrations of Lavender extract by MTT assay method. Morphological studies were performed via microscopic analyses. Flow cytometry and proteomics techniques were applied to determining pharmaceutical mechanism of lavender cytotoxic effects. The survival and morphological studies revealed anticancer characteristics of extract. Flow cytometry findings indicate that Lavender extract had a cytotoxic effect upon the cell line. Proteomics analysis identified a significant alternation in gastric cellular proteome expression after treating with the extract. Among 1000 spots, more than 700 spots showed changes in protein expression levels by informatics analysis. Of these proteins, expression of three cancer biomarkers, Annexin1, Anolase1 and HSP70 were suppressed by extract. This study suggests that Lavender extract is cytotoxic and alter protein expression in a gastric cancer cell line.