Crunchyroll's senior management will maintain a stake, along with investor TV Tokyo.
Terms were not disclosed.
Crunchyroll was founded in San Francisco in 2007 and launched two years later.
In March, it said it had more than 200,000 premium subscribers. They pay $7 to $12 a month for high-definition streaming, discounts on merchandise and immediate access to new episodes after airing. The company launched an online store in May.
Chernin said in a statement that the plan is to continue to grow the anime channel while launching new channels in different genres.