Major League Baseball 2K9 is a simulation of the sport of baseball. The heart of the game is the franchise mode where the player can play whole seasons with its hundreds of matches and a managerial part. Besides keeping the balance, there are three main activities in this part: studying extensive statistics, player trading and hiring players through free agents. The latter is similar to other sports games: every player has other wishes for his team, e.g. athletic success. If the player's club can fulfill these wishes better the club has to pay less salary. Trading however is handled differently: Every club gives a value to the players on the roster. This value influences how the trading plays out. Training is another important part to consider.

Matches can either be simulated or played manually. Every part of the match has its own control scheme: For pitching the player uses two parts of his input device: the first for aiming and the second to recreate a movement (depending on the used move). Batting is done by swinging the bat in the right timing. He can also influence the ball's direction in the way he hits it. During fielding the player basically tells the controlled player the direction in which he should throw the ball. Besides the franchise mode the player can participate in training, Home Run Derby and Postseason mode (play-offs). Players can unlock training cards.

The are a few small differences between the versions: on the Wii the player controls batting and pitching directly with the remote and the nunchuck and the PSP version features slightly different fielding controls. In the franchise mode the player can manage up to four franchises in the PS2 version and there is a farming system on PSP.