We introduce a topological data analysis (TDA) framework to characterize departure‐delay co-occurrence in Japan’s domestic airline networks. By constructing a delay‐based filtration on daily delayed flight networks for All Nippon Airways (ANA) and Japan Airlines (JAL), we track how airports form delay co-occurrence loops through persistent homology using Vietoris–Rips complex filtration technique. We find JAL’s network is more fragmented, while ANA shows wider, longer-lasting delay loops before