In early 2000, the Government of Bengkalis Regency established a higher education institution under the name Naval Polytechnic of Bengkalis (Politeknik Perkapalan Bengkalis) through the Gema Bahari Foundation. It offered three study programs, including Ship Electrical System, Ship Construction, and Ship Machinery. During its development, Naval Polytechnic of Bengkalis changed its name to Polytechnic of Bengkalis (Politeknik Bengkalis) and was under the auspices of the Bangun Insani Foundation (YBI) of Bengkalis. It offered five study programs, including Naval Architecture Engineering, Mechanical Engineering, Electrical Engineering, Civil Engineering, and Business Administration.

In July 2001, Polytechnic of Bengkalis accepted the first batch of students. In 2006, Polytechnic of Bengkalis added two study programs, including Business English and Informatics Engineering.

In early 2008, Polytechnic of Bengkalis requested support from the Bangun Insani Foundation, the Government of Bengkalis Regency, and the Regional House of Representatives of Bengkalis Regency to propose a status upgrade from Private Higher Education (PTS) to State Higher Education (PTN).

In 2009, Polytechnic of Bengkalis along with the Bangun Insani Foundation, and the Government of Bengkalis Regency proposed a status upgrade from PTS to PTN to the Ministry of National Education through the Directorate General of Higher Education.

On February 9, 2011, Polytechnic of Bengkalis along with the Bangun Insani Foundation and the Government of Bengkalis Regency delivered a presentation to the Minister of State Apparatus Empowerment and Bureaucratic Reforms to complete the eligibility to be a state polytechnic.

On July 29, 2011, Polytechnic of Bengkalis officially became PTN under the name State Polytechnic of Bengkalis (Politeknik Negeri Bengkalis) through the Regulation of the Minister of National Education (Permendiknas) No. 28 of 2011 regarding the Establishment, Organization and Work Procedure of State Polytechnic of Bengkalis.

On December 26, 2011, State Polytechnic of Bengkalis was inaugurated by the Minister of Education and Culture of the Republic of Indonesia.

In 2013, State Polytechnic of Bengkalis added two study programs, including D4 Production and Maintenance Mechanical Engineering and Electrical Engineering; and three Study Programs Outside Domicile (PDD), including D2 Welding Engineering, D2 Electrical Power Generation System Engineering, and D2 Computer Accounting.

In 2014 and 2015, State Polytechnic of Bengkalis added two study programs, including D4 Road and Bridge Design Engineering and D3 (Nautical, Technica, Engineering & Shipping Management).

In 2016, State Polytechnic of Bengkalis added several study programs, including D4 Software Engineering, D4 International Business Administration and D4 Public Finance Accounting.