It started its operation in 1989 at Concepcion Elementary School as Marikina High School Concepcion Annex with Ms. Lagrimas B. Garcia as the first Head Teacher In-charge and was followed by Ms. Victoria Naranja as the Head Teacher In-Charge and Dr. Lydia Timotheo followed in S.Y. 1999-2000.

Since there was no available site for the school, it was reverted to Marikina High School in June 1995-1998. Upon the initiative of the MHS prinicipal, Ms. Florencia M. Lopez, and with the approval of the Mayor Bayani Fernando, Concepcion High School was temporarily housed at SSS Village Elementary School in June 1998. It created 411 first year high school students and 14 teachers with Ms. Victoria Naranja as the Head Teacher In-Charge and Dr. Lydia Timotheo followed in S.Y. 1999-2000.

The school was transferred to its permanent site in Malanday in September 2001 with Dr. Timotheo as the first principal. It was in 2002 that it had its first Graduation ceremonies. From 2003 up to 2008, Mr. Edgardo Nieto took the helm as principal and was followed by Mr. Wilfredo S. Jabal in June 2008 - July 2010; Mr. Alberto D. Villamor in July 2010-July 2012; Ms. Lagrimas B. Garcia in July 2012 - August 2014.

In 2007, under Mr. Edgardo, the school gradually shifted to Strengthened Technical Vocational Program (STVEP), making MNHS the only Tech - Voc school in the Division of Marikina City.

By virtue, RA 9655, Concepcion High School was officially renamed Malanday National High School through the efforts of then Congressman Marcelino R. Teodoro.

In August 2014, Dr. Albert B. Mutia took the cudgels as the principal who bannered the physical transformation of the school to answer the needs of its students and teachers. In 2016 in compliance to the Enhanced Basic Education Act, MNHS opened its Senior High School Program with General Academic Strand (GAS) and Tech-Voc Track (Bread and Pastry Production NCII, Food and Beverage Services NCII & NCIII, Hair Dressing NCII, Electrical Installation and Maintenance NCIII & NCIV, and Shielded Metal Arc Welding NCII) as the field of specialization. It was in April 2018 when MNHS produced its first batch of SHS graduates.

On October 1, 2020, Ms. Nerissa S. Estrella took the responsibility of leading MNHS as the OIC-Principal. Her first day marked several firsts: the onset of distance learning brought about by the global pandemic, October as the first month of the school year, the introduction of eCommerce strand in SHS, and the majority of TVL teachers as writers of Self Learning Modules (SLMs). As the distance learning commenced, Ms. Estrella successfully managed and facilated the creation, printing, and distribution of school-based Self Learning Modules (SLMs) for the TVL specialized and mandatory subjects for modular learners.

MNHS being situated along the river has proven itself to be resilient in the face of devastating typhoons and floods. But through the unity and cooperation of school officials, teachers, staff, and generous external stakeholders, MNHS always bounces back and continues to improve to better serve its learners.

As a Tech-Voc school, Malanday National High School works towards continous improvement to help bring out the best in the learners and prepare them for a successful career and a productive life in the future.