The Scientific Career System was first institutionalized through Executive Order No. 784 on March 17, 1982 by the late President Ferdinand E. Marcos. It was formally organized on July 19, 1983 with the issuance of Executive Order 901 Prescribing the Rules and Regulations to Implement the Scientific Career System. The System was initiated at the National Science and Technology Agency (now the Department of Science and Technology) being the primary agency in the field of scientific and technological development. Through Presidential Decree No. 1416, the Civil Service Commission was tasked to administer the implementation of the System with DOST as its co-implementor.

The System was further strengthened through the enactment of the Republic Act 8439 or the Magna Carta for Scientists, Engineers, Researchers and other Science and Technology Personnel in the Government which provides benefits and allowances to conferred scientists under the System pursuant to Section 5 of said law.

The System is now being administered by the National Academy of Science and Technology (NAST) which also houses the Scientific Career Council Secretariat.