Brogan was seeking a second term as Education Commissioner when, in 1998, Jeb Bush asked him to be his running mate as lieutenant governor.

As lieutenant governor, Brogan oversaw education policy and acted as legislative liaison for the Bush administration.

During Brogan's initial six-year term, the university developed its first-ever comprehensive strategic plan, which has provided a roadmap for progress since its inception in 2006.

He oversaw the largest physical development of the university's campuses as new facilities were built to serve FAU's undergraduate and graduate population, which surpassed 27,000 for the first time.

During his tenure, relationships with the Florida Legislature were restored, as evidenced by the landmark governance agreement of 2010 that provided clarity regarding oversight of the university system.

The board approved a new 2025 Strategic Plan that includes 39 key performance benchmarks, which is an integral part of Florida's nationally recognized accountability framework that tracks progress of university and system goals.

The board and Legislature worked together to implement a number of top priorities, including establishing a path for universities to reach preeminent status, creating the nation's first fully online institute operated by a public research university, and providing a platform for a performance-funding model that fosters the unique mission of each institution while advancing system goals.

[6] [7] Under his leadership of the PASSHE, the membership of the faculty union, APSCUF, which represents more than 5000 teachers, went on strike for the first time in 34 years, after working for more than 13 months without a contract.