In this study, we propose a method to estimate body composition-related health indicators (e.g., ratio of body fat, body water, and muscle, etc.) using video-based gait analysis. This method is more efficient than individual measurement using a conventional body composition meter. Specifically, we designed a deep-learning framework with a convolutional neural network (CNN), where the input is a gait energy image (GEI) and the output consists of the health indicators. Although a vast amount of training data is typically required to train network parameters, it is unfeasible to collect sufficient ground-truth data, i.e., pairs consisting of the gait video and the health indicators measured using a body composition meter for each subject. We therefore use a two-step approach to exploit an auxiliary gait dataset that contains a large number of subjects but lacks the ground-truth health indicators. At the first step, we pre-train a backbone network using the auxiliary dataset to output gait primitives such as arm swing, stride, the degree of stoop, and the body width — considered to be relevant to the health indicators. At the second step, we add some layers to the backbone network and fine-tune the entire network to output the health indicators even with a limited number of ground-truth data points of the health indicators. Experimental results show that the proposed method outperforms the other methods when training from scratch as well as when using an auto-encoder-based pre-training and fine-tuning approach; it achieves relatively high estimation accuracy for the body composition-related health indicators except for body fat-relevant ones.