The only known prey of the Megamouth Shark are epipelagic and mesopelagic euphausiid shrimp, copepods and jellyfish (Yano et al. 1997). The feeding structures of this shark may allow it to feed on other pelagic invertebrates and even small fishes, but so far the stomach contents studied suggest that it primarily targets euphausiid shrimp (Compagno 2001).

Observations made on a live-captured megamouth shark which was later tagged with an acoustic telemetric tag and tracked for two days, suggested it could breathe readily by gill-pumping and was not dependent on constant swimming like other lamnoid sharks. During the tracking period, the shark revealed a pattern of vertical, crepuscular migration in the epipelagic zone. It has been suggested that the Megamouth Shark may follow vertical migrations of euphausiid prey during diel cycles (Compagno 2001).

The mode of reproduction is probably aplacental viviparous with uterine cannabilism or cannibal vivipary suspected in the form of oophagy. A late immature or early adolescent female had two ovaries with many tiny oocytes, while an adult female had numerous larger oocytes. This is similar to the ovaries of other lamnoids.