The school first opened in 1962 as Marymount College, a women's junior college founded by the Religious of the Sacred Heart of Mary (RSHM). Due to financial hardship Marymount College sought to sell the books of its library. Donald E. Ross visited the campus to purchase the library, but was so inspired by the school he decided to stay and help it succeed. In 1971, a period of transition began, and the school was placed under the control of a lay board. At that time, Donald E. Ross was named president. In 1974, the name was changed to the College of Boca Raton. The college was granted accreditation at Level II in 1986. In 1988, it was accredited at Level III. During this time, it was transformed from a two-year school to a four-year college with a master's program.

Entrance of Lynn University in Boca Raton
The College of Boca Raton became Lynn University in 1991 to honor its benefactors, the Lynn family.

In 2003–2004, Donald E. Ross was paid a salary of over $5,000,000, making him at the time the highest-paid college or university president in the nation. Lynn University retained the national accounting firm KPMG to determine an equitable retirement compensation package for Ross considering his performance and 35-year term of service ("More than $4.5 million was put aside for his planned June 2006 retirement – an influx of cash designed to make up for decades of no retirement benefits" being allocated due to budget concerns). This was a third of the endowment for the university. On July 1, 2006, Ross retired after 35 years as the university's president; Kevin M. Ross succeeded his father in office.

On October 22, 2012, the university hosted the third and final 2012 U.S. presidential debate between U.S. president Barack Obama and former Massachusetts governor Mitt Romney concerning U.S. foreign policy. The debate was held at the Keith C. and Elaine Johnson World Performing Arts Center and was moderated by journalist Bob Schieffer of CBS News.
Who was the highest-paid College president in 2003-2004 in U.S.?
In 2003–2004, Donald E. Ross was paid a salary of over $5,000,000, making him at the time the highest-paid college or university president in the nation.