In a method of cleaning and sterilizing an ultrapure water manufacturing system including an ultrapure water manufacturing apparatus, a point of use of ultrapure water, and an ultrapure water channel connecting the ultrapure water manufacturing apparatus and the point of use and a cleaning and sterilizing process including an alkali cleaning step for cleaning at least part of the inside of the system with alkaline solution and a sterilizing step for sterilizing the system with sterile water after the alkali cleaning is treated twice or more. By treating the cleaning and sterilizing process twice or more, metals, organic substances, particles, and bacteria inside the ultrapure water manufacturing system can be highly efficiently removed and thereby ultrapure water satisfying required water quality can be produced within a short period of time after the cleaning and sterilizing.
