The Mekong giant catfish Pangasianodon gigas is endemic to the Mekong River basin, and is recognized as endangered species, largely due to overfishing and development of the river basin. We monitored food intake of P. gigas in a stable environment in an aquarium over a 6-year period and analyzed their feeding rhythm and fasting periods. The daily food intake for each fish was recorded from 18 June 2004 to 17 June 2010. The feeding rhythm or pattern was determined by the fast Fourier transform (FFT) analysis. The FFT analysis revealed that different cycles of feeding rhythm (168.8, 313.1, and 365.3 days) in three catfishes and no observable cycles in two catfishes. However, three catfishes showed subordinate peaks with approximately 365 days (365.3 days for all). These suggest that, at least, four of five catfish had have approximately 365-days feeding cycle. We also showed that all catfish undergo long-term fasting periods (> 20 days). Of note, the feeding/fasting pattern coincides with the wet/dry seasons in Thailand, which also corresponds to the abundance of the catfish food resource (Cladophora spp.). We found that P. gigas exhibit a seasonal feeding rhythm that is synchronized by food availability. Furthermore, we found that the seasonal feeding rhythm was gradually dampened over time, suggesting that the observed seasonal feeding rhythm with long-term fasting of the catfish is likely controlled by an endogenous clock system. To our knowledge, this is the first case of quantification of the seasonal feeding rhythm with fasting periods in teleost fish.