Dynamical behaviors of complex interacting systems, including brain activities, financial price movements, and physical collective phenomena, are associated with underlying interactions between the system's components. The issue of uncovering interaction relations in such systems using observable dynamics is called relational inference. In this study, we propose a Diffusion model for Relational Inference (DiffRI), inspired by a self-supervised method for probabilistic time series imputation. DiffRI learns to infer the probability of the presence of connections between components through conditional diffusion modeling. Experiments on both simulated and quasi-real datasets show that DiffRI is highly competent compared with other state-of-the-art models in discovering ground truth interactions in an unsupervised manner. Our code will be made public soon.