Breast cancer is the most commonly diagnosed cancer, which alone accounts for 30% all new cancer diagnoses for women, posing a threat to women’s health. Segmentation of breast ultrasound images into functional tissues can aid tumor localization, breast density measurement, and assessment of treatment response, which is important to the clinical diagnosis of breast cancer. However, manually segmenting the ultrasound images, which is skill and experience dependent, would lead to a subjective diagnosis; in addition, it is time-consuming for radiologists to review hundreds of clinical images. Therefore, automatic segmentation of breast ultrasound images into functional tissues has received attention in recent years, amidst the more numerous studies of detection and segmentation of masses. In this paper, we propose to use convolutional neural networks (CNNs) for segmenting breast ultrasound images into four major tissues: skin, fibroglandular tissue, mass, and fatty tissue, on three-dimensional (3D) breast ultrasound images. Quantitative metrics for evaluation of segmentation results including Accuracy, Precision, Recall, and Symbol, all reached over 80%, which indicates that the method proposed has the capacity to distinguish functional tissues in breast ultrasound images. Another metric called the Jaccard similarity index (JSI) yields an 85.1% value, outperforming our previous study using the watershed algorithm with 74.54% JSI value. Thus, our proposed method might have the potential to provide the segmentations necessary to assist the clinical diagnosis of breast cancer and improve imaging in other modes in medical ultrasound.