A medical image processing apparatus includes: a superimposed image generation unit configured to generate a superimposed image by superimposing a subject image and a fluorescent image in areas corresponding to each other; a determination unit configured to determine whether or not at least one of a subject and an observation device moves from timing before timing at which one of the subject image and the fluorescent image is captured to the timing; and a superimposition controller configured to cause the superimposition image generation unit to prohibit a superimposition in an area of at least a part of the subject image and the fluorescent image when the determination unit determines that at least one of the subject and the observation device moves.