The Uganda Pentecostal University originated from the Grotius School of Law and Professional Studies, which started in February 2001. It commenced its operations in February 2001 when it admitted its first student in law at its first campus in Mengo, Kampala. At the time it operated as an independent institution affiliated to Busoga University but separate in its management. The institution continued to operate as such until July 2004, when the National Council for Higher Education (NCHE) offered Grotius School of Law and Professional Studies a license to set up a University but directed and obligated it to seek suitable partners so as to fulfill the conditions set by the NCHE.

 The partner that was found was the United Pentecostal Churches International of Uganda (UPCIU) to which most of the founders of Grotius School of Law and Professional Studies belong. UPCIU provided the University with land including buildings in Fort Portal Municipality, Mubende Town Council, Mbarara Municipality and in Masaka district. The university held its first graduation on Thursday June 8, 2006 at the main campus in Fort Portal.