His contract when he arrived in January 2012 called for a base salary of $950,000. That's going up to $1.9 million starting July 1, the school said Thursday.
Counting compensation for radio and television work and a Nike contract, O'Brien's total deal this year would be worth more than $3.2 million.
O'Brien guided the Nittany Lions to an 8-4 record after the program was hit by landmark NCAA sanctions for the Jerry Sandusky sex-abuse scandal and player defections weeks before the start of the 2012 season.
"In the face of great adversity, Bill did a tremendous job with all facets of the Penn State football program," athletic director Dave Joyner said in a statement.
University President Rodney Erickson said he and Joyner talked about revising O'Brien's contract at the end of the season.
"And these discussions moved forward with my blessing and involvement," Erickson said in a statement.
The base salary would drop to $1.1 million in 2014 before a raise to $1.6 million in 2015. The former offensive coordinator of the New England Patriots would then be eligible for a 5 percent raise starting in 2016.
The revised contract also reverts the length of the deal to the term agreed last January—through the conclusion of the 2016 season.
Penn State had announced after the sanctions were announced last July that O'Brien had a clause in his contract that called for the deal to be extended by the length of sanctions. A team spokesman confirmed the contract released Thursday supersedes that clause.
The sanctions include a four-year bowl ban, which would expire after the 2015 season, and a $60 million fine to paid in five annual installments ending in 2016.
The team is also limited to 65 scholarship players—20 less than allowed for FBS schools—for a four-year period starting in 2014 and ending after the 2017-18 academic year.
"This rightly recognizes Bill's outstanding achievements in guiding our student-athletes on and off the field," said Joyner, who was not taking additional questions Thursday about his contract.
O'Brien drew interest from NFL teams including the Eagles and Browns following the 2012 season in which he electrified Penn State's offense with schemes resembling the high-scoring attack of the Patriots.
Quarterback Matt McGloin set several school passing records and wideout Allen Robinson emerged to become the Big Ten's top receiver. Tight end turned into a position of strength, while "Linebacker U" defensive schemes were tweaked to become more aggressive.
O'Brien said in January that he while he spoke with clubs, no job was ever offered. Since then, O'Brien has switched agents from Joe Linta to Neil Cornrich. The Associated Press left a message Thursday with Cornrich's office.
The amended contract specifies a buyout clause if O'Brien bolts for the NFL, worth his current year's base salary times the number of years left on his contract. It's less than the buyout clause for other reasons, which includes the radio/TV and Nike deal compensation into the equation.
Also, O'Brien could get an annual bonus of up to $200,000 based on the team's performance. His initial contract allowed for such a bonus based mainly on the Nittany Lions' postseason success— a meaningless clause given the Big Ten championship game and bowl bans.
O'Brien replaced Hall of Fame coach Joe Paterno, who was fired in November 2011 in the aftermath of Sandusky's arrest on child sex abuse charges. Paterno died about two weeks after O'Brien was hired in January 2012.
In the latter part of his 46-year career, Paterno was dogged by inquiries about retirement, though leaving for the NFL wasn't really an option. Last year, Penn State valued Paterno's compensation at just more than $1 million—a comparative bargain for a coach with two national championships on his resume. Alabama's Nick Saban, for instance, makes more than $5 million a year.