Hidden Expedition: The Uncharted Islands is a hidden object game and the fifth entry into the Hidden Expedition series of "seek and find" games. The gameplay is similar to previous instalments, with the focus being on finding items scattered across a diverse collection of scenes. Some items are placed in the player's inventory and need to be used in other locations to advance in the game. The game does feature some variations on the basic hidden object formula, with many hidden object scenes being two screens wide, and some items only being revealed by the manipulation of other items.
The hidden object sections are broken up by mini-games, often in the form of puzzles, in a way similar to earlier entries in the series. These puzzles can be skipped, and an in-game hint system can be used to help find hard to locate items.
The game opens with the player having crashed on a desert island that is being terrorized by an evil pirate, Captain Undertow, who is intent on stealing the inventions of one of the island's inhabitants, Gideon, and escaping the islands to enslave the world. The player is given the task of saving the inhabitants of the island from Undertow and thwarting his plot. The game is a direct sequel to Hidden Expedition: Devil's Triangle, and several locations and characters from that game reappear in this one.