Satureja khuzistanica Jamzad is a valuable and endemic medicinal plant. Boron and zinc are essential elements for the vegetative and reproductive growth of plants and have significant effects on yield, essential oil composition and the seed production of plants. To investigate the effects of the foliar application of zinc and boron on the growth, yield, seed production and phytochemical properties of S. khuzistanica, a study was conducted in a factorial experiment with three replicates in two consecutive years based on a randomized complete block design. The foliar application of boron (B) at three concentrations (control or distilled water, 0.4% and 0.8% as H3BO3) and zinc (Zn) at three concentrations (control or distilled water, 0.3% and 0.6% as ZnSO4) was carried out. Our results showed that the foliar application of B resulted in a significant increase in the fresh and dry weights of plants, the dry weight of stems, drug yield, seed yield, seed germination and 1000-seed weight. At the same time, the application of B resulted in a significant decrease in seed emptiness. The fresh and dry weights of plants, drug yield, seed yield, 1000-seed weight and seed germination were also significantly improved by Zn foliar spraying compared to the control. Application of 0.8% B resulted in a significant decrease in seed emptiness by 14.16% and 22.37%, as compared to the control. The foliar spraying of B and Zn improved the total phenolic content, the essential oil content and the yield and antioxidant activity of S. khuzistanica. Moreover, B application generally concentrated more carvacrol in the essential oil (in the first experimental year). In contrast, no significant differences were observed between Zn treatments in carvacrol content and total flavonoids. The use of several microelements, such as B and Zn, could improve both the quantity and quality of S. khuzistanica. Additionally, improvement of seed set and seed quality by the foliar spraying of Zn and B may be useful for growing plants in arid and semi-arid areas.