The PFCS is governed by a Board of Directors composed of fifteen representatives from the five member societies. Each member society annually designates three of its board members including its president as its representative to the PFCS board. The PFCS board elects a president, vice president, secretary, treasurer, and auditor to serve a term of one year.
- Organizes the annual Philippine Chemistry Congress,
- Coordinates the activities of the five Chemistry Societies during Chemistry Week which is celebrated on the third week of February every year; provides financial support to students through the Philippine Association of Chemistry Students (PACS) for their Chemistry Week activities,
- Provides financial support for the publication of KIMIKA, the official research journal of the KKP,
- Provides permanent office space and support staff to member organizations, and
- Publishes the Philippine Chemistry News, a newsletter which contains updates of the activities of the member societies as well as articles on current issues.