Sonic Advance 3 maintains the fast paced, side scrolling gameplay from previous entries in the Sonic Advance franchise. The game borrows mechanics introduced in Sonic Advance 2
such as the aerial trick system and faster moving characters.
New to this entry in the series is the ability to select a team of two characters rather than just one. The first character selected is player controlled, while the second allows the player to activate a specific "tag ability" upon holding and releasing the R button. Although there are five characters to choose from, leading to twenty possible permutations, each combination is classified into one of three categories: Speed, Flight, and Power. This category is determined by the focus of each team's abilities. The levels are specifically designed to have branching routes that cater to each category of team.