The rat was discovered soon after the Loong Air flight left the eastern city of Hangzhou and was headed for the southwestern city of Xishuangbanna in Yunnan Province.
According to the airline, which plies more than 50 domestic routes, it was unclear how the rodent gained access to the plane.
The airliner confirmed it was not a domesticated pet and they were looking into how it got on the plane, state-run Xinhua news agency reported, adding the rodent may have arrived with the catering service.
Rats are infamous for damaging a plane's electrical and other systems by chewing through wires, creating panic among passengers and leading to huge safety issues.