The statistical analysis covers a four-year period for the academic years of 2008-09 through 2011-12. The football team's multi-year APR score was a team-record 993, trailing only Northwestern (996).
The score is up from last year's total of 989, which ranked tied for second nationally with Duke, and behind Northwestern (995).
"Our commitment to excellence at Boise State extends beyond competition," Director of Athletics Mark Coyle said. "We strive for success in the classroom, and I am extremely proud of the work our student-athletes, coaches and support staff put in to make that a reality at Boise State."
The APR provides a real-time look at a team's academic success each semester by tracking the academic progress of each student-athlete on scholarship. The APR accounts for eligibility, retention and graduation, providing a measure of each team's academic performance.
Last week the Broncos' football team was honored with a Public Recognition Award from the NCAA for having its multi-year score rank in the top-10 percent of FBS schools, the third-consecutive year Boise State has received the accolade.
Boise State is one of only four schools to receive the honor in each of the last three seasons, a list that also includes Clemson, Northwestern and Ohio State.
In addition to football, Boise State's men's cross country (990), men's indoor track and field (985), men's outdoor track and field (979) and swimming and diving (991) programs also recorded scores that led the Mountain West.
Football, men's indoor track and field, men's outdoor track and field and swimming and diving were four of eight Bronco programs to set team records for four-year APR. Others included women's golf (992), soccer (986), softball (963) and wrestling (950).
Additionally, 10 of Boise State's programs had perfect 2011-12 single-reporting year scores of 1,000: women's basketball, men's cross country, women's cross country, women's golf, men's tennis, women's tennis, soccer, softball, volleyball and wrestling.
As a department, Boise State earned an overall score of 977, meaning the school earned 97.7 percent of possible points over the last four years.