Major League Baseball 2K6 is an update of its previous years' version, featuring roster updates as well as a three year report of all the teams and players in the game. It also featured a brand new movement system as well as realistic player crashes and a morale system, where the better the player is, the more their teammates will perform better as well.
Gameplay includes standard modes such as exhibition, season, as well as a new feature letting players take on the role of an international team in the World Baseball Classic. Players can also challenge umpires if they feel a call has been botched, which can affect the teams' morale for better or worse.
The game features TV broadcast "flashback replays" giving it a real feel of a TV presentation, with commentary from Jon Miller and Joe Morgan. The Xbox 360 version had virtually the same graphics as previous generations, with some extra dialogue and commentary. Derek Jeter endorsed the game and appeared on all console and handheld releases.
Each console version has online capabilities, allowing players to download their friends' profiles using V.I.P. They can view each other's stats and results of their games, gaining an advantage in online matches.