Visayan spotted deer have a fine, dense and soft dark-brown coat on their upper body. They have spots on their backs and flanks, which they retain throughout their life. They have pale white fur on the underside as well as on the chin and lower lip.

Visayan spotted deer are small, the shoulder height of a mature deer is around 75 to 80 cm. Females are much smaller than the males. The ears and tail are relatively short.