Custom Robo takes place in a collect-customize-and-battle style RPG genre similar to games such as Robotrek or Front Mission, but with frantic action battles in confined 3D arenas (2D arenas in Custom Robo GX), similar to Virtual On. In each game's story mode, players slip into the role of a nameable young boy who has just had a dream about Custom Robos. After waking up, he walks up to his parents while they talk, and proceed to give him his first robo and some parts for battling. A friend then comes by to take the protagonist to where Custom Robo events are held. In each game, the first Custom Robo players obtain is always a model of the Ray series. The goal for players is to improve their skills and collect different custom robos in order to defeat everyone, including champion robo users.
Perhaps the most important aspect of gameplay is the customization: the player is required to choose from his collected parts to build his own unique fighting machine. The system is designed to be both simple and challenging. A Custom Robo is equipped with 3 weapons : A gun (right hand) , a bomb (left hand) , and a pod (on the robo's back). There are also numerous robo chassis to choose from , and leg parts that affect the robo's movement.
In Custom Robo battles, the object is to reduce the opponent's hit points from 1000 to 0 by using different robos, guns, bombs, pods, and charge attacks. Custom Robos are arranged in groups that are similar to their abilities. The endurance bar is located above the player's hit points in battle; once it runs out, the Custom Robo gets "downed" which means that it stays fallen for a couple seconds. After the Robo gets up, it goes into "rebirth" mode, where it stays invincible for about 3 seconds. Having one's own hit points reduced to 0 first results in a Knockout or "KO". If players repeatedly lose the same battle, the game will offer the option of reducing the opponent's initial health, in order to make the battle easier. If players continue to lose several times, the degree of handicap offered increases up to 75%, giving the opponent a starting HP of 250, rather than 1000.