Summer squash seed yield and quality can be improved by the application of boron (B) and fruit set-order, which might affect fertilization and pollination. Two field experiments were performed during the summer seasons of 2021 and 2022 to investigate the effects of foliar application of boron at levels of 0, 25, and 50 ppm for two times (after 45 and 60 days from the planting date) and different fruit-set orders on seed yield, yield components and quality in summer squash of two genotypes, Shmamy and Cope. The twelve treatments were arranged in a randomized complete block design (RCBD) with a split plot arrangement with three replicates. The results of the current study revealed that foliar application of B at 50 ppm improved seed yield components, such as fruit weight, seed weight per fruit and the number of seeds per fruit, leading to a significant increase in total seed yield in the two studied genotypes of summer squash. Also, the B application at 50 ppm increased the seed quality parameters, oil content, crude protein content and total antioxidant activity in both genotypes during the two seasons. In addition, this research revealed that fruit-set order had a significant effect on total seed yield, seed yield components and seed quality. Whereas, the fruits in 2nd and 3rd order have achieved the highest means of all seed yield components, total seed yield and seed quality parameters in both studied genotypes and during both seasons, compared to the fruits in 1st and 4th order. In light of current results, it would be recommended that applying B at 50 ppm as a foliar spray treatment and keep the fruits in second or third order to improve the total seed yield and seed quality of summer squash plants.