Nitrogen (N) effect on crop yield depends on several factors such as soil type, climatic characteristics and orchard management, including plant density and N fertilization. These variables can be used to develop yield prediction models, which are scarce in the horticulture sector. This study aimed to evaluate the effect of nitrogen fertilization, orchards and cultivars and to predict the yields of ‘Royal Gala’ and ‘Fuji Suprema’ apples cultivated in a subtropical climate under different soil N availabilities. During the four seasons, nitrogen fertilization was applied a rates of 0, 25, 50, 100 and 150 kg N ha−1 year−1 for ‘Royal Gala’ and ‘Fuji Suprema’ apples located in southern Brazil. Yield, average fruit weight and leaf and fruit pulp N concentration were evaluated. Yield prediction models were developed based on the following variables: concentration of N in leaves and fruits, air temperature, chilling units, relative humidity and rainfall. “Cultivar” was the variable responsible for the greatest variation of yield, followed by “years/season”, and then the “orchard management. The N rates applied in the four seasons did not predict crop yield. In the model, “orchard” was the greatest determinant for leaf N concentration, and “season” was the main determinant for fruit-pulp N concentration. Mathematical model (3), based on leaf and fruit pulp N concentration, and certain climatic variables (minimum air temperature, annual rainfall and chilling hours < 7.2 °C) had the greatest potential for predicting yield in orchards of ‘Royal Gala’ and ‘Fuji Suprema’.