The game is the sixth overall installment of the Bases Loaded series, and third installment of the secondary trilogy for the Super Nintendo. Super Bases Loaded 3 was licensed by the Major League Baseball Players Association (MLBPA) and uses real MLB players, but it wasn't licensed by Major League Baseball (MLB). All 28 U.S. cities that had a MLB team at the time are listed but team names and logos are not given. No real stadiums are used and the World Series is renamed the championship tournament.

Notable baseball players in the game include: Barry Bonds, Kirby Puckett, and Tony Gwynn.

For many aspects of gameplay, such as fielding and base-running, the game offers players a choice between automatic and manual control. For example, a player who opts for manual control of his team's fielders will, when catching a fly ball, have to move the fielder of his choice into position to make the catch. Unfortunately, due to a flaw in the scrolling system used during plays, the fielding team's outfielders are often off screen, often making it extremely difficult to successfully complete a play in manual mode.

The game has also been criticized for the audio samples used to voice its umpire, characterized by some as incongruous and/or inappropriately effete. In particular, the samples used when calling strikes (and strikeouts) have been likened to the Yes Guy (a character from The Simpsons, who was in turn based on a character created by Frank Nelson).

One major flaw in the game is that one pitch, the split-finger fastball, cannot be hit if it is thrown high in the strike zone. A perfect game with 27 strikeouts can be thrown at will by using only this pitch. Only a handful of pitchers in the game can throw the pitch, however.