The New York-based investor said in a regulatory filing that Freshpet's shares, down nearly 60% so far this year, are undervalued.
Jana Partners has a history of pushing for change in the food and beverage industry.
Register now for FREE unlimited access to Reuters.com RegisterJana Partners has also been pushing for changes at packaged food maker TreeHouse Foods Inc (THS.N) since last year.
Freshpet has not yet spoken to Jana, but will "look forward to hearing their perspectives", the company said in an emailed statement.
The news of Jana's stake was first reported by the Wall Street Journal.