Cebu Doctors' University (formerly known as Cebu Doctors' College) applied for an initial permit to offer a Bachelor of Science in Pharmacy Program to the Commission on Higher Education (CHED) last October 27, 2003, under the College of Arts and Sciences. They intend to offer the program on its Osmeña Boulevard, Cebu City campus. The initial program adapted an Associate in Health Science Education (ASHE) Based Curriculum leading to the Bachelor of Science in Pharmacy (B.S. Pharmacy) degree.

Upon the primary visit of the Regional Quality Assessment Team (RQAT), they recommended the appointment of a Dean and its respective office. Dr. Leticia G. Cabrera, with a Master's degree in Pharmacognosy and Doctorate in Pharmaceutical Science, was appointed as the first dean of the College of Pharmacy last April 1, 2004, after a thorough interview with Dr. Potenciano V. Larrazabal, Jr., the University President and Chairman of the Board then. After successful compliance with RQAT recommendations, CHED authorized CDU to offer subjects at the first-year level. The College of Pharmacy was instituted and started to provide the program with only the subjects in Level I of the 4-year B.S. Pharmacy Curriculum, having only 14 students. The B.S Pharmacy Curriculum was enriched, realigned, and approved by CHED Region VII last June 9, 2004, and September 7, 2005.

By December 14, 2005, the Institution applied for a permit to offer Levels II, III, and IV for the Academic Year (A.Y.) 2006 – 2007 to CHED. The College's teaching staff were only three (3) faculty members, including the Dean.

The University's new campus at North Reclamation Area, Mandaue City, was completed in the Summer of 2007, with the College of Pharmacy Office on the 4th floor. Dr. Cabrera was not only the Dean of the College of Pharmacy but was also assigned as the Head of the Research Office. As the College grew, more faculty members were hired to teach. On November 26, 2007, the CHED recognized the Cebu Doctors' University – College of Pharmacy (CDU-CP). The first batch of B.S. Pharmacy students of the College graduated last March of 2008. In the 2nd Semester of A.Y. 2007-2008, the College had a total population of 97 students from the first to fourth year. In the same academic year, a newly revised Curriculum based on the CHED CMO No. 03 series of 2006 was implemented. By March of 2008, the College was visited by three Deans of Philippine Association of Colleges of Pharmacy (PACOP) member schools resulting in the admission of CDU-CP to PACOP. Around the first half of 2010, Dr. Cabrera was succeeded by Dr. Jennilyn C. Corvera as the Dean of the College. Dr. Corvera officially started her office last August 2010.

Effective Academic Year 2010 – 2011, the B.S. Pharmacy Curriculum was revised in compliance with CHED CMO No. 03 series of 2006. By 2012, another minor revision was made to the curriculum effective A.Y. 2012 – 2013. Concurrently, the College Office was moved to the Ground Floor.

In March 2020, physical classes were suspended because of the COVID-19 pandemic. Hence, all students and employees transitioned to an online learning modality adapting the current Learning Management System of the University, CDU's Electronic Learning Online (+ and more), most popularly known as CeLo+. The Philippine Association of Colleges and University Commission on Accreditation (PACUCOA) visited the College virtually last September 30 to October 1, 2021. However, after the sudden passing of Dr. Corvera last October 3, 2021, the University's Administration appointed Mr. Jan Harmony A. Cesar as the Officer-in-Charge (OIC) Dean effective October 8, 2021-July 31,2022 and Dean last August 1, 2022. At the moment, CDU College of Pharmacy was granted Level 1 Candidate Status last November 6, 2021, with validity until November 2023.