The third entry in the Tokimeki Memorial series follows the same story template as its predecessors: the protagonist is a male high-school student, and his goal is to win the affection of one of the several available female interests. This time, the school in question is Moegino High, and the suggested "main" love interest is called Yukiko Makihara.

Tokimeki Memorial 3 differs from its predecessors in graphical style: it is the first in the series that utilizes character animation and 3D cel-shaded graphics.

The gameplay in Tokimeki Memorial 3 underwent certain changes compared to the previous games. One of the main changes is a simplification of the complex statistics system. The hero has only three main parameters in this game: strength, willpower, and stress. Progress with a girl is measured by levels, similarly to role-playing games. Otherwise, the game still retains the simulation approach, and includes the traditional schedule-making, date-choosing, and participating in various school and leisure activities. The protagonist can also wear different clothes, have different hobbies, and even dedicate his time to playing video games.