The Department of Special Collections and Manuscripts (1990-1999) collected and preserved rare and important materials including: books, pamphlets, prints, photographs, manuscripts, diaries, journals, papers, music scores, and university records. In 1990, the Harold B. Lee Library Special Collections department and the Archives and Manuscripts department were combined to create the Special Collections and Manuscripts department. The Chair of Special Collections and Manuscripts was Scott Duvall (1990-1999). In 1997, Scott Duvall was appointed Assistant University Librarian for Special Collections. He acted as both department Chair and Assistant University Librarian from 1997 to 1999. The Department of Special Collections was located on the fourth floor of the Harold B. Lee Library, where reading rooms serviced faculty, students, and visitors with the opportunity to use the artifacts in Special Collections. In 1999, due to a generous donation, the department was moved to the basement of the Library and renamed L. Tom Perry Special Collections.

The L. Tom Perry Special Collections (est. 2000) is a special collections library and manuscripts/archival repository.

The Perry Special Collections was named in May 2000, and was previously known as the Department of Special Collections; Manuscripts. Aline and L. Sam Skaggs, through their ALSAM Foundation, made a generous financial donation to the new library and requested that the Special Collections be named after L. Tom Perry, an apostle of the Church of Jesus Christ of Latter-day Saints. The department is responsible for collecting, preserving, and making available rare books, historical manuscripts, and university records. Department chairs have included Scott Duvall (1999-2002), P. Bradford Westwood (2002-2009), Russ Taylor (2009-2014), J. Gordon Daines III (2014-2020), and Thomas R. Wells, (2020- ).