The fundamental aspects of gameplay are unchanged from Ouendan to Elite Beat Agents. The stages of Elite Beat Agents are presented in a comic book fashion. After the introduction to a character and their problem, the agents are deployed and the action begins. The play mechanics involve performing one of three actions with the stylus in various combinations.
- Hit Markers - Operated by tapping numbered circles.
- Phrase Markers - Operated by tapping and holding the stylus on a ball within a circle while following it along a path.
- Spin Markers - Operated by spinning the stylus around the on-screen disc until bars on both sides light up.
To successfully perform each action one must complete it as a timed circle converges on each main circle. The timing follows the rhythm of the music. The Hit and Phrase markers must be hit in numbered sequence. The markers are arranged in 'tracks' which range from one to about fifteen markers in length. Success is monitored by the "Elite-O-Meter", a gauge at the top of the touch screen that is constantly draining at a rate based on the difficulty level. Successful actions, such as tapping the Hit Markers in sync with the music, will keep the gauge filled, while missing a marker will partially deplete the gauge. If the meter empties completely, the stage ends prematurely in failure. The first three levels of Breezin' mode feature an on-screen indicator to highlight the order in which the markers must be hit.
Each stage is divided into multiple gameplay sections separated by story sequences, the specific number of which varying by stage. If the Elite-O-Meter is in the yellow when the player reaches one of these breaks, the story will depict the person in need making significant progress towards his or her goal. If it is in the red, the scene will instead depict the person encountering a setback. In between breaks, during the gameplay, the top screen shows the person attempting to accomplish what they need to do at that time. The scene depicted changes every beat, or when the markers switch color, depending on the player's progress. If the player scores an "Elite Beat" by scoring 300 points on each marker in a single beat, then the person makes a lot of progress very enthusiastically. If the player scores a "Beat" (no score lower than 100, but not all 300), the person will be shown making average progress on their goal. However, if the player does not score a special beat bonus at all by scoring a 50 on a marker or missing it entirely, the person on the top screen will encounter difficulties and setbacks. The player will receive bonuses to the final grade and unlock artwork for completing a stage with positive outcomes at all stage breaks.
Elite Beat Agents has the ability to save replays and shows how many Elite Beats and Beats the player hit during a song.
Each stage has three possible endings for its story. The ending depends on the number of gameplay sections passed. If all gameplay sections are passed the story will have the best ending, with the main character succeeding in its challenge. If at least one section is passed, but not all of them, then the story will have the average ending, where the main character succeeds with moderate success. If all sections are failed, however, the story will have the worst outcome,where the main character finishes his or her endeavor but still fails.
High scores are acquired by achieving combos, or stringing together a series of successful actions. The longer the player is able to maintain a combo, the greater the multiplier applied to each successful action. Should the player miss a marker completely, the multiplier will stop and the player must start a new one. The game keeps track of individual stage high scores for all difficulty levels, as well as a cumulative high score that affects the player's "Agent Rank." The Agent Rank is a special title such as "Soldier of Song" or "God of Groove" that will change as the player's cumulative high score reaches specific milestones. Elite Beat Agents features three bonus stages that are unlocked when three such ranks are achieved.
The player's performance in each stage is rated on a letter-grade scale, with "D" being the lowest possible rank and S being the best. To achieve an S-rank in a level, at least 90% of all beats must be 300, another 9% must be at least 100, and no more than 1% may be 50. The player must end with a "Perfect", obtained by missing no beats throughout the entire song. However, it is possible to break a combo by missing a dot on a Phrase Marker track and still get an S-rank. Due to the nature of the game's scoring mechanic, it is possible to achieve a new high score in a stage while simultaneously earning a lower grade than the previous high score performance, although this is somewhat rare.
A few additional features have been introduced to Elite Beat Agents from the game play in Ouendan. Primarily, these include the ability to reveal more statistics about a player's performance when they complete a song; the ability to save their performance as "ghost" data that they can later use in a "Vs. Ghost" multiplayer mode; the ability to review the last few moments of a failed performance, and the ability to skip the musical introductions to stages.