The New Era Educational Institute (NEEI) was formally opened on June 17, 1975 by virtue of GPR No. 232, Series of 1975 issued by the Ministry of Education, Culture and Sports (now known as the Department of Education). NEEI initially offered secondary education in Echague (now Carlos Palanca Street), Quiapo, Manila. On June 6, 1977, pursuant to the requirements of the Corporation Law (Republic Act 1459), NEEI was declared as a private, non-stock, non-profit, non-sectarian educational institution. The year 1978 saw the opening of NEEI’s collegiate course offerings at the Evangelical College (EVCO) building along Don Mariano Marcos (now Commonwealth) Avenue, Diliman, Quezon City. Upon the conferment of degrees to 12 collegiate graduates in 1981, the school became known as the New Era College (NEC). On May 10, 1986, the permanent building for NEC was inaugurated, situated in a wide expanse of land along St. Joseph Street, Milton Hills Subdivision, Diliman, (now known as #9 Central Avenue, New Era) Quezon City. NEC was granted 'University' status by the Commission on Higher Education (CHEd) on June 30, 1995, thus adopting its present name, New Era University.

As part of the celebration of New Era University's 25th anniversary, the New Era University – Lipa City Branch was established on May 5, 2000 in Batangas. The school, located in a four-hectare land, initially offered Preschool and Elementary Education. The Secondary Education Program, the K to 12 Curriculum with the Senior High School Program, and the School of Graduate Studies (SGS) were implemented accordingly. Recently, NEU – Lipa held the launching of the iOS Sign Language Application and Certification Program for Sign Language Interpreters. Adding to its victories, was the granting of government recognition for the Bachelor of Science courses: Accountancy, Accounting Technology, Real Estate Management, and Entrepreneurship as well as the newly applied courses: BS Computer Science, BS Computer Engineering, Bachelor of Technical-Vocational Teacher Education, and BS Psychology.

New Era University's first branch outside Metro Manila is situated in a sprawling six-hectare campus in the City of San Fernando, Pampanga. New Era University – Pampanga City Branch was established on June 25, 1994. The school initially offered Preparatory and Elementary Education Programs followed by the Secondary Education Program and is now offering Collegiate Programs in the branch – Bachelor of Elementary Education and BS Business Administration.

New Era University opened its New Era University – General Santos City Branch in June 1994, at first offering the Preschool Education Program. Elementary and Secondary Education Programs were opened soon after. It was on June 5, 1998, when the new school building situated in a half-hectare land area was inaugurated. The school is now fully equipped to implement the K to 12 program with Senior High School. NEU – GSC marked another significant event of its history in March 2018 upon receiving Government Recognition for the Bachelor of Science courses: Real Estate Management, Entrepreneurship, Accounting Technology, and Accountancy.

The New Era University – Rizal Branch is the fifth and newest branch of the University. The campus occupies a fifty-hectare tract of hilly land in Pinugay, Baras, Rizal close to the foot of the majestic Sierra Madre Mountain Range and near the famous limestone formation conservation area, Masungi Georeserve. The campus' terrain ranges from flat to undulating to sloping, which are either open or covered with trees. A stream also traverses the campus. On June 30, 2017, the groundbreaking ceremony of the two-story main building of the campus was held. The branch was granted government recognition by the Commission on Higher Education (CHED) on March 7, 2022 and the pioneer batch under the Bachelor of Science in Agriculture program held their first official class on January 7, 2019.