The total nonstructural carbohydrate (TNC) concentration is an important indicator of the growth period and health of fruit trees. Remote sensing can be applied to monitor the TNC concentration in crops in a non-destructive manner. In this study, hyperspectral imaging from an unmanned aerial vehicle was applied to estimate the TNC concentration in apple trees. Partial least-squares regression, ridge regression, and Gaussian process regression (GP) were used to develop estimation models, and their effectiveness using selected key bands as opposed to full bands was evaluated in an effort to reduce computational costs and improve reproducibility. Nine key bands were identified, and the GP-based model using these key bands performed almost as well as the models using full bands. These results can be combined with previous studies on estimating the nitrogen concentration to provide useful information for more precise nutrient management to improve the yield and quality of apple trees.