The conducted experiment evaluated the effects of three fungi—Trichoderma atroviride (Ta), Trichoderma harzianum (Th) and Phytium oligandrum (Po)—on the growth of maidens of two apple cultivars, ‘Szampion’ and ‘Topaz’, budded on two rootstocks, M.9 and M.26, in the nursery. The evaluation was based on the number of maidens obtained and their height, trunk diameter and number and length of lateral shoots, as well as the fresh weight of the leaves and the whole maiden. For the weaker-growing maidens of the ‘Topaz’ cultivar, the activity of the photosynthetic apparatus was additionally measured depending on the rootstock and fungal treatments. The number of maidens obtained improved significantly when Th (8.3–9.0%) and Po (8.4–12.8%) were applied, depending on the rootstock and cultivar used. With the best treatment with the Po fungus, on average, for the two cultivars, maiden apple trees budded on the M.9 dwarf rootstock were characterized by a significantly better height of 6% and trunk diameter of 13% compared to the control. In contrast, trees grown on the M.26 rootstock did not have significantly increased growth after the same treatments, with the exception of the Po fungus, which improved the stem diameter by an average of 10%. The use of fungi stimulated an increase in the number and length of the lateral shoots of maidens of the more easily branching ‘Szampion’ apple tree cultivar. Based on the fluorescence parameters obtained, it can be assumed that the ‘Topaz’ cultivar on the M.26 rootstock is less susceptible to stress conditions, especially those related to high temperatures and drought. All fungi used had a positive effect on the activity of the photosynthetic apparatus. Significantly worse values of the fluorescence parameters were obtained for the control combination compared to the fungal treatments.