Abstract: Orchard automation has attracted the attention of researchers recently due to the shortage of global labor force. To automate tasks in orchards such as pruning, thinning, and harvesting, a detailed understanding of the tree structure is required. However, occlusions from foliage and fruits can make it challenging to predict the position of occluded trunks and branches. This work proposes a regression-based deep learning model, Hallucination of Occluded Branch Convolutional Neural Network (HOB-CNN), for tree branch position prediction in varying occluded conditions. We formulate tree branch position prediction as a regression problem towards the horizontal locations of the branch along the vertical direction or vice versa. We present comparative experiments on Y-shaped trees with two state-of-the-art baselines, representing common approaches to the problem. Experiments show that HOB-CNN outperform the baselines at predicting branch position and shows robustness against varying levels of occlusion. We further validated HOB-CNN against two different types of 2D trees, and HOB-CNN shows generalization across different trees and robustness under different occluded conditions.