Kennesaw State finally achieved University status in 1996. The Kennesaw State's baseball and softball teams won the NCAA Division II national championships in 1996. The winning Owls continued excelling in athletics, including the Lady Owls 2003 win of the NCAA Women's Division II Soccer Championship and the men's basketball team win of the 2004 NCAA Men's Division II Basketball Championship. In part due to their winning Division II in 2005, the Owls joined Division I and the Atlantic Sun Conference.
In 2004, KSU was recognized by the Department of Homeland Security and the National Security Agency as a National Center of Academic Excellence in Information Assurance Education. At the time, this placed KSU among 67 other institutions recognized as CAE/IAEs with this recognition. KSU was recognized again in 2007.
In the summer of 2006, Daniel S. Papp became the university's third president.
KSU also began its first doctoral programs in Education in Leadership for Learning, Education, and a doctorate of Business Administration.
On November 1, 2013, the University System of Georgia announced that Kennesaw State University would merge with nearby Southern Polytechnic State University in 2015. Kennesaw State would be the surviving institution, with President Papp serving as president of the merged university. Southern Polytechnic was started by the president of the Georgia Institute of Technology, Blake R. Van Leer who was known for making Atlanta the "MIT of the South." On January 6, 2015, the Georgia Board of Regents of the University System of Georgia approved the consolidation of Southern Polytechnic State and Kennesaw State. In honor of SPSU's legacy, Kennesaw State established Southern Polytechnic College of Engineering and Engineering Technology as one of its 11 colleges.
On January 1, 2015, Kennesaw State University was classified by the Carnegie Foundation for Teaching and Learning as a Community Engaged Institution.
In the Fall of 2016, students and faculty protested the suspected appointment of Georgia's Republican attorney general, Sam Olens, as the next Kennesaw president. He took office on November 1, 2016, resigning as attorney general. He left office in February of 2018. Pamela Whitten was KSU's next president, serving until 2021. On March 16, 2022, Kathy Schwaig was named the sixth president.
KSU's Computer Science and Information Systems department hosts the Center for Election Systems, which certified and monitored the direct recording electronic machines used in Georgia elections until June 2018 at the latest. This shift was initiated due in part to poor security by the center, which had accidentally exposed over 6.5 million voter records.