The species, which is under China's highest level of protection, is hunted by poachers because of a secretion believed to have high medicinal value and is a precious ingredient in some perfumes.
The deer were released to a habitat in Ningshan County the Qinling Mountains in Shaanxi Province, the provincial forestry department said.
It marks the beginning of China's restoration of the wild population, said Wang Weisheng, an official with the State Forestry Administration.
The 13 deer have developed strong survival abilities, including avoiding predators and identifying human threats, during a year of training, said Li Sanyuan, director of the provincial forestry department.
In 1970s and 1980s, the wild population declined significantly due to poaching and damage to its habitat. The situation has improved in recent years.
There are 4,000 to 4,500 forest musk deer living in the wild and over 13,000 living in captivity in Shaanxi.