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The Island of Dr. Brain is mostly a point and click game, although at times, the keyboard may be used. Additionally, aside from the lagoon jigsaw puzzle, there are no time constraints. However, even the jigsaw puzzle, although timed, does not get scored based on solving time. Scoring is mostly based on difficulty. There are three difficulty levels: Novice, Standard, and Expert. The difficulty can be changed at any time, but puzzles solved at a harder difficulty will earn more points.

The maximum amount of points that can be earned is 1000. With the exception of the map puzzle at the very beginning, which always earns a gold plaque, puzzles solved on novice level earn 5 points, intermediate 10 points, and expert 15 points. The raw score is calculated by adding up the points for the highest difficulty level each puzzle was solved on. For the 26 puzzles, the maximum raw score is 15 x 26, or 390 points.

After the first time a puzzle is solved and points are awarded based on difficulty, an additional 1 point of extra credit will be given for the next four times a puzzle is solved on other difficulty levels and for the next three times it is solved on the level it was initially solved on. In other words, points can be earned for the first four times played on each difficulty setting, with the first time solved earning 5, 10, or 15 points and the next times earning only 1 point. The exception to this rule is the word search, which will award extra credit points for the first seven times played at each difficulty for a total of 20 extra credit points. A maximum of 287 extra credit points can be earned.

The third part of scoring is related to your hint watch. The hint watch is a device which will give you a hint to a puzzle if you are stuck; however, it has a limited amount of battery life, so it can only be used so many times. Every time a puzzle is solved, assuming it is one where points are earned, one charge is added to the hint watch. At the end of the game, if the hint watch was never used, 9 bonus points are awarded. The most points that can be awarded this way is 323.