The company wants to focus on a new marketing effort that will appear mostly online.
Pepsi beverages have been advertised in the Super Bowl since 1987.
However, snack food unit Frito-Lay will still advertise.
The company was one of the biggest advertisers last year, buying several minutes of commercial time.
Ad time last year cost about $3 million for 30 seconds, on average.
The Feb. 7 NFL championship game will be televised on CBS.
Package delivery company FedEx also said Thursday it will not advertise again in the Super Bowl due to costs, the same reason the company gave last year for sitting it out.
