Many of the active constituents of drug or medicines were originally derived from medicinal plants. Iranian Borage are still being used in regular basis. Selenium (Se) is an essential mineral nutrient for animal and human growth. The aim of this research was to determine the effect of (2, 4, 8 and 16 mg L−1) of as sodium selenate (Na2SeO4) and as sodium selenite (Na2SeO3) on some important properties of Iranian Borage in factorial based on Randomized Complete Block Design via four steps: 2 true leaves stage, ten leaves, 2 weeks and 1 week before flowering. The traits were evaluated during flowering period. Results showed that the highest shoot fresh and dry weight and shoot length, total alkaloid, essential oil percentage were obtained by 4 mg L−1 sodium selenate at the end of flowering. In addition, 4 mg L−1 sodium selenate concentration significantly improved flower yield (diameter, number, weight). The plants were treated with 8 mg L−1 sodium selenate, the higher total phenols and flavonoids, antioxidant activity, soluble sugars, root and fresh weight was seen at end of flowering. When the plants were sprayed with 4 mg L−1 sodium selenite higher total chlorophyll was observed at full of flowering. 16 mg L−1 sodium selenite released the maximum Se acclimation in the petals. 20 composites were discovered containing ɑ-Pinene (23.61%) with sodium selenate in 4 mg L−1. Generally, selenium sources significantly improved morpho-physiological and phytochemical.