The flame, which is the substance of the whole PSHS logo, symbolizes the enthusiasm, ardor, light and warmth of the PSHS community. The flame is seen in the center of the four circles paired together with alternating colors of blue and white. This is the common symbol of the DOST and its agencies, one of which is the Philippine Science High School System.
The circles symbolize unit particles, the building blocks of nature, which are the subject and substance of science and technology. The circle design gives an illusion of movement, signifying progress through Science and Technology.