Megamouth sharks Megachasma pelagios Taylor, Compagno, and Struhsaker, 1983, are a large-bodied, planktivorous, deep-sea species with peculiar morphology. Since their initial description in the late 20th century, many individuals of different sizes have been reported, but few studies examined ontogenetic changes in body shapes. Here, we assess the growth changes in their heads and fins based on length measurements from nine different-sized individuals (177–544 cm in total length). Bivariate analyses showed that the head becomes larger relative to body length with increasing body size (i.e., positive allometry), whereas the relative size of the caudal fin remains constant (i.e., isometric growth). This trend differs from basking sharks and apparently resembles whale sharks and some baleen whales, although they are all large-bodied filter feeders. Given that relative mouth size is linked to feeding modes, our results suggest that megamouth sharks have different feeding modes from ram-feeding basking sharks and may have some similarity with suction-feeding whale sharks and engulfment-feeding baleen whales.