Selenium (Se) malnutrition in humans is caused by low soil Se availability, leading to an insufficient content of this nutrient in food. In this study, we examined the effect of Se fertilisation on the absorption and distribution of Se in apple (Malus domestica Borkh.) trees, as well as fruit quality and storability. The experiment was carried out on mature ‘Red Jonaprince’ apple trees grown in medium-textured soil. Fertilisation of Se (as sodium selenate) was applied as: (i) summer sprays, 4 times in a season at a rate of 50 g Se ha−1, (ii) a fall spray, 2 weeks before harvest at a rate of 200 g Se ha−1, (iii) soil application at a rate of 500 g Se ha−1, and (iv) fertigation at a rate of 100 g Se ha−1. Trees that were not fertilised with Se served as controls. The results revealed that the fall Se spray caused leaf burns and defoliation, but it did not affect tree vigour and fruit yield. The highest leaf Se concentration was found on Se-sprayed trees in the fall. Most Se in fruit was recorded on Se-sprayed trees in the fall and on Se-fertigated trees; fruit Se amounts from these combinations covered about 30 % of the recommended daily intake. None of the Se treatments affected fruit appearance (mean weight, skin russeting, and colour), flesh firmness, and acidity at harvest. Apart from the fall Se spray, the other treatments decreased the soluble solid concentration (SSC), starch index values, ethylene evolution, and increased Streif index values in apples at harvest. After storage, Se-enriched apples were firmer, contained more organic acids, and produced less ethylene than the control fruit. We conclude that Se fertigation or a fall Se spray can be recommended in apple orchards, at least for late season and winter varieties, to biofortify fruit with Se and delay their ripening process.