Certification is a formal process whereby a community of knowledgeable, experienced, and skilled representatives of an organization, such as INCOSE, provides formal recognition that a person has achieved competency in specific areas (demonstrated by education, experience, and knowledge). Certification differs from licensing in that licenses are permissions granted by a government entity for a person to practice within its regulatory boundaries. Certification also differs from a "certificate" that documents the successful completion of a training or education program.

The International Council on Systems Engineering established its Professional Certification Program in March 2004 to provide a formal method for recognizing the knowledge and experience of systems engineers through the "Certified Systems Engineering Professional" designation. Certification is valid for three years from the date awarded, and may be renewed in three-year intervals. The original CSEP examination was based on the INCOSE Systems Engineering Handbook Version 2A. In 2008, the exam was updated to reflect Version 3.1 of the handbook, which is based on the international systems engineering standard ISO/IEC 15288.

The program was expanded to multiple levels of certification in 2008. Now the INCOSE Certification Program has an entry level “Associate Certified Systems Engineering Professional” for junior or recently graduated engineers who do not yet have the requisite years of SE experience. Upon achieving at least five years of SE experience the ASEP can transition to CSEP. INCOSE is also developing a senior-level “Expert Systems Engineering Professional” designation for systems engineers with significant experience and demonstrated systems accomplishments. It will be available in 2009.

In 2008, the certification program added its first extension for professionals that work in the United States Department of Defense acquisition environment. This extension, designated CSEP-Acq, is earned by taking an additional acquisition exam based on the Defense Acquisition Guidebook, Chapter 4 on Systems Engineering, in addition to the standard CSEP exam.