Micronutriens deficiency is prevalent in case of drought stress conditions, so complementary boron and zinc nutrition are important for crops to overcome drought stress. This study evaluated the effect of zinc and boron foliar application on physiological traits of sesame under different irrigation levels. The experiment was conducted as a split plot in a randomized complete block design with three replications at Fars Research Center for Agriculture and Natural Resources in 2013. The main factor included three irrigation levels (irrigation after 75, 110 and 145 mm evaporation from class A evaporation pan) and sub-factor included foliar spraying water, zinc sulphate, boric acid and application of the mixture of zinc sulphate with boric acid. Results showed that proline content of leaf significantly increased by foliar application of boric acid in 75 mm evaporation treatment and by boric acid and mixture of zinc sulphate and boric acid in 110 and 145 mm evaporation treatments. Maximum Glycinebetaine was acquired by foliar zinc sulphate application in all three irrigation levels. Foliar application of zinc sulphate and boric acid helped to obtain the highest leaf relative water content compared to control. Maximum seed zinc content in 75 mm evaporation treatment was obtained from zinc sulphate and the mixture of zinc sulphate with boric acid application. Generally, results showed that foliar application of zinc sulphate and boric acid improved physiological traits of sesame, especially under drought stress so the plant can tolerate the impact of drought stress better.