Minesweeper Flags is based on the Minesweeper game that is included in some versions of Microsoft Windows. Players must locate mines on a minefield by first selecting an initial square which they believe does not contain a mine. If they are successful in finding one without a mine, it will reveal some squares around it that also do not contain mines, some of which will be blank, but some will have numbers in them. These numbers reveal how many mines are located around that square, but will not give you any hint as to where they are or how far away they are. The player must now use this information to identify the rest of the squares that do not have mines in them (marking). If the player is successful, the entire board can be cleared and the bombs can be secured. If the player however selects a square with a mine in it, the mine will detonate and it will be game over. There is a counter at the bottom that helps determine the amount of mines and a general timer to show how long it is taking you.
Unlike the original 2D Minesweeper, Flags' grids are themed 3 dimensional, with you having a semi top-down view of the playing field. Game modes included are the classic single player game and the same mode in multiplayer (player taking turns selecting a square, the first to land a mine loses the game). There are loose matches and a campaign mode that stretches along the seven continents with different matches. In the campaign mode puzzles are not always square. There are sometimes multiple lives, shown through a heart indicator near the top of the screen. It also includes an all new multiplayer only mode called "Flags", in which the mines are replaced by various coloured flags, but unlike with the original game, you are trying to find, not avoid, them, and you have to find them before your opponent. The rules can be customized based on the turn time limit, the number of players, the difficulty level, and altering two conditions where another move is provided when a flag is found, and the ability to win early.