The establishment of Christian Colleges of Southeast Asia (CCSA) was a vision of its founder, Dr. Michael T. Ang, Sr., PME to reach out to the youth by putting up a school that can provide quality Christian Education up to the tertiary level. This was realized in January 2003 when CCSA was formally organized with Engr. Michael T. Ang, Sr., PME as Chairman of the Board of Trustees along with Mr. Leonito A. Fabian, MM as the Executive Vice-President and Administrator.

CCSA started operations in S.Y. 2004-2005. Its initial offerings were: Complete Preschool Program; Grades I and II; First and Second Year High School; and First Year Level of the five college programs.

Before the end of its first year of operation, Technical Education and Skills Development Authority (TESDA) granted CCSA permit to operate a 6-month Caregiver Course NC II.

On its second year, CCSA offered complete programs for preschool, grade school and high school.

In S.Y. 2007-2008, CCSA offered the Open High School Program later called as Sunday School. In the same year, CHED granted Government Recognition for the four college programs, namely: Bachelor of Science in Elementary Education, Bachelor of Science in Secondary Education, Bachelor of Science in Commerce and Bachelor of Science in Computer Science.

On its fifth year of operation, in S.Y. 2008-2009, the BS Mathematics Program and the Sunday High School Program were given Government Recognition by CHED and DepEd respectively.

In May 2009, Dr. Rosita V. Fundador was appointed by the Board of Trustees as Director of the School of Basic Education.

On January 09, 2010, CCSA held the ground breaking ceremony for the construction of its own five storey Basic Education building on a 2-hectare lot in Ma-a, Davao City.

On April 27, 2010, CHED granted CCSA permit to offer BS in Entrepreneurship, BS Accountancy, BS Accounting Technology and Bachelor of Technical Teacher Education.

In June 2011, CCSA School of Basic Education transferred to the permanent school site in Ma-a Davao City.

The School Year 2012-2013 started with a significant change as the School of Basic Education implemented the K to 12 Program.

In April 2014, Engr. Michael T. Ang, Sr. was conferred with the honorary doctorate degree of Doctor of Ministry by Alliance Graduate School of Quezon City, Metro Manila.

After the death of Dr. Michael T. Ang, Sr. on August 26, 2014, the Board of Trustees elected Engr. Carlos T. Ang as the new Chairman and President in January 2015. He now leads the institution in its active participation in the globalization of education.

On May 21, 2015, CCSA was granted provisional permit to operate the Senior High School Program offering the Academic Track and Technical-Vocational Track.

On May 19, 2016, The ACSCU-Accrediting Agency, Inc. granted CCSA Level I status for its Preschool, Elementary and Junior High School Programs, covering the period May 2016 to May 2019.

In March 2018, President Carlos T. Ang, on behalf of the Board of Trustees of CCSA, appointed Mrs. Anne Y. Hechanova, CPA, as the Officer In-Charge of the School of Basic Education and then later appointed as the SBE Director.

On May 23, 2019, CCSA was granted by ACSCU-ACI, its Level II Re-Accredited Status covering then period April 2019 to April 2022 for its Preschool, Grade School and Junior High School levels.