In 1969, the PSHS produced its first batch of alumni.  This batch and four immediately succeeding batches plunged headlong into the turbulent period of student activism in the early seventies.  Organizing homecomings was of little concern to the alumni and this was left to the PSHS administration.  Nevertheless, these early homecomings were well attended.

The first homecoming organized by the alumni was in 1983, under the leadership of Mario Taguiwalo ’69, and hosted by batches ’73 and ’78.  Held at the PSHS Canteen (the gymnasium had not yet been built then), Balik-Science’83 featured an address by Director Cleofe M. Bacuñgan, musical numbers by Jacqui Magno and the Tux ( Bob Serrano of batch’78 was a Tux member), the usual raffle draws, and the first elections for the PSHS AA Board of Directors.

The alumni were formally organized into an association following the elections, holding its first board meeting on September 11, 1983, calling itself the Philippine Science High School Alumni Association (PSHS AA).

On February 12, 1998, Republic Act No. 8496 created the Philippine Science High School (PSHS) System wherein one of its critical provisions was the creation of  a PSHS System Board of Trustees (BOT), specifically calling out among its members, the President of the PSHS National Alumni Association.  And so it happened that in Y2005, a PSHS  System National Alumni Association was founded to address the representation of the alumni in the PSHS System BOT.  Dr. Reynaldo B. Vea was elected Chairman and Rene Abad President.  Subsequently, Rene Abad as NAA President took his seat as a member of the Board of Trustees of the PSHS System as provided by law.

In 2007, the PSHS AA and the PSHS NAA started talks,  acknowledging the need to merge and unify. The merger was approved in the 2nd half of 2008 by the respective members of the PSHS AA and PSHS System NAA .The Unified NAA was able to hit the ground running, so to speak, as the alumni/alumnae of the PSHS Diliman Campus (the largest alumni base) was immediately harnessed.  With broadened membership, the Association would now be able to pursue activities and projects with high impact and visibility.