The elements selenium (Se) and iodine (I) are both crucial for the normal functioning of the thyroid. Biofortification with these elements is particularly feasible in areas where they show a deficit. Iodine and selenium can have positive effects on different plants when applied at the correct concentrations. The effects of their simultaneous addition on plant physiology and biochemistry, as well as on seed germination and sprout biomass, were studied in pumpkin (Cucurbita pepo L. ssp. pepo). To study the effect of Se and I on sprouts, sprouts were grown from seeds soaked in solutions of different forms of Se, I and their combination in the growth chamber experiment. In the field experiment, pumpkins plants were foliarly treated with the same concentrations and forms of Se and I. The combination of Se and I treatments enhanced the germination of the soaked seeds, with no significant differences between Se and I treatments for sprout mass. The yield of pumpkins and seed production were unaffected by Se and I foliar application. The anthocyanin levels and respiratory potential measured via the electron transport system’s activity showed different patterns according to treatments and plant parts (sprouts, leaves, seeds). The redistribution of Se and I from seeds to sprouts was significant. The accumulation of Se was higher in sprouts from the seeds treated with Se together with I, compared to sprouts from the seeds treated with Se alone. Interactions between Se and I were also noted in the seeds, which developed in the treated plants.