GuitarFreaks is played using a controller designed to imitate the shape of an electric guitar, most like the Fender Jazzmaster or Fender Mustang. The neck houses three buttons, colored red, green, and blue. On the main face of the guitar, a pick lever is used to simulate the picking and strumming of an actual guitar. A small metal knob near the pick is used to alter the sound produced by the game, such as adding Chorus/Delay effects.
The interface is similar to other games in the Bemani series. Two note scrolls—one for each player—are displayed at the left and right sides of the screen. Colorful animations for each song are displayed in the center of the screen. Each note scroll consists of four columns: one each for the red, green, and blue buttons, and a fourth column, known as the Wailing Bonus column. Individual notes and chords are represented by small colored bars that scroll upward in the columns. To play the correct note, the player must hold down the buttons corresponding to the colored bars, and move the pick lever when the bars reach the yellow picking line. When a guitar icon is displayed in the Wailing Bonus column along with an associated note, the player can tilt the guitar upright while playing the note to receive bonus points.
The player's accuracy is judged for each note played. The current system uses the names Perfect, Great, Good, Poor, and Miss to indicate a player's accuracy. Ratings of Poor or Miss will deplete the player's Groove Gauge, while Perfect and Great ratings will replenish it. If the Groove Gauge is emptied completely, the player fails, and the game ends. Players are allowed to play anywhere from one to five songs depending on the game cabinet's configuration, with the ability to earn additional songs in certain versions of the game
Upon successful completion of a song, players are graded on their performance. When the game ends, the player's total score across all songs played is tabulated.
Because the second version of GuitarFreaks was released prior to the first version of DrumMania, GuitarFreaks is one "mix" number higher than the DrumMania version it links up to. For example, GUITARFREAKS 6thMIX is designed to be linked with DrumMania 5thMIX. The mix versions were synchronized with the release of GuitarFreaksV & DrumManiaV eschewing the long-standing number system, and replacing what would have been the 12th and 11th mix, respectively.
As with DrumMania, the current version of GuitarFreaks features 500 songs in total. Most songs are either crossovers from other Bemani games, and J-pop and J-Rock. Some mixes also contain covers of popular North American songs.