Cosmic Encounter Online (CEO) was the official online version of Cosmic Encounter, released in 2003. The game could be played over the internet by up to four players, with bots filling in empty spots. As of 2010, the game had 35 aliens, some of which were designed specifically for online play. As it was in the format of a computer game instead of a board game, CEO's terminology differed from the terms of the other versions; for example, cards were called "pods."
35 aliens were available, including six new aliens and three specifically designed for online play. Six aliens (Clone, Macron, Oracle, Trader, Warrior, Zombie) could be used by guests or free members; the others were only available to paid subscribers.