Shrub willow is a valuable source of hardwood biomass feedstock which is used for the production of bioenergy, biofuels, and renewable bio-based products. The biomass produced from this short-rotation woody plant can be used for heat and electricity generation. Thus, an accurate estimation of shrub willow above-ground biomass (AGB) is of paramount importance. This paper aimed to estimate shrub willow AGB using multi-spectral unmanned aerial system (UAS) imagery and machine learning techniques. To accomplish this goal, a machine learning model (i.e., random forest (RF)) and a deep learning method (i.e., convolutional neural network (CNN)) were applied to the spectral bands and some vegetation indices over a site in Camillus, NY, US in July 2019. The results demonstrated the superiority of the RF model (RMSE of 1.73 Mg/ha and R2 of 0.95) compared to the CNN (RMSE of 2.69 Mg/ha and R2 of 0.89) technique. Adding vegetation indices to spectral bands and using a convolutional approach for training purposes could significantly improve the modeling efficiency.