BYU consistently receives national recognition for its strong undergraduate and graduate programs. U.S. News & World Report ranks BYU's Marriott School of Management and the J. Reuben Clark Law School in the top 40 in the country.

In the July 2002 edition of the Chronicle of Higher Education, BYU was recognized as the best in the nation at turning research dollars into inventions and new companies. Some notable inventions originating at BYU include a drug for treating a rare form of leukemia, water modeling software, and the modern word-processor. Philo T. Farnsworth developed some of his ideas for the creation of the television while attending BYU. Harvey Fletcher, a BYU alumnus, went on to carry out the now famous oil-drop experiment with Robert Millikan, and was later Founding Dean of the BYU College of Engineering.

BYU is on the list of censured administrations of the American Association of University Professors due to past violations of the generally recognized principles of academic freedom and tenure as recognized by the AAUP. BYU has been on this list since 1998. The AAUP report states that "the climate for academic freedom at Brigham Young University is distressingly poor". The president of BYU at the time of the investigation and censure left office in 2003; the AAUP has subsequently sent the new president a description of the steps needed to have the censure removed.