In Haikyū!! Cross Team Match! the player takes on the part of the lead and only volleyball team player of Momojihara High School. The protagonist attends a Karasuno conducted joint rehearsal and communicates with characters from Haikyuu's mange/anime universe. Based on the interactions players can then be hired to form a squad.

In certain situations a special event occurs such as a practice game to hire someone, or the appearance of a special item when the confidence meter gets to a certain level. Matches are largely determined by the players' statistics, but they are played in real-time. Prompts appear to quickly select a specific player, for instance for the reception, and lines are drawn for other types of moves.

There is an additional plot called Shimada Mart after the player finishes the main story.