Jolly Jam is a tile based puzzle game where the player has to remove jellies of different colours from the game board. This is done by creating boxes by drawing a line between two jellies of the same colour that will then make up a box. This will lead to all jellies within the box that matches the colour of the corner jellies to be removed. After they are removed other jellies fall down and take their place and if four jellies of the same colour form a square these too will be removed. For every level a certain amount of jellies of specific colours have to be removed and this has to be done within a certain number of moves.
In addition to the ordinary jellies there are also special jellies that are created when a larger number of jellies are removed in the same box. Special jellies are activated when boxed and will affect other jellies in various ways, for example clearing a row or all jellies of the same colour. Special jellies are also created and activated when the player has leftover moves at the end of a level. There are also various special tiles such as ice that sometimes also have to cleared. Sometimes monsters will appear which can jump around on the board. These are cleared in the same ways as other tiles. Some levels feature boss fights. To defeat the boss damage has to be done by removing jellies of specific colours.
The player can also use various boosters that are unlocked by completing levels. Once unlocked a few uses are available, then more has to be bought with diamonds which is the game's currency. There are three different boosters: the golden spoon boost that removes a single jelly or monster, the jelly cross that removes a row and a column and the jellyfier which turns a normal jelly into a special jelly. The game also features a life system where each lost level costs a heart. When all out of hearts the player has to wait for them to recharge or pay to acquire more.