As a federation, PHILFEJA consists of charter associations of former students, graduates, grantees and trainees of Japanese schools, technical institutions, colleges and universities and who are bound by their common advocacy of promoting friendship, understanding and interpersonal exchange between the Philippines and Japan. These associations are:
- Philippine Association of Japanese Governments Scholars, Inc. (PHILAJAMES) organized in 1972
- The Philippine Cultural and Technical Association of Returned Overseas Scholars (PHILCULTAROS) organized in 1965
- Association of Philippine Private Alumni of Japanese Universities (APPAJU) organized in 1991
- Samahan ng mga Pilipinong Nakapag-aral at Nanirahan sa Nippon (SAPILNIP) organized in 1993
- JICA Alumni Association of the Philippines, Inc. (JAAP) reorganized in 2013 following its merger with the Philippines-Japan Fellows Association (PHILJAFA) and other JICA alumni associations.
Organizations that have become inactive but were at one time charter associations of PHILFEJA are:
- OMNI Ventures – an association organized by the former wartime Filipino students to Japan (1943-1945), which was among the pioneer-founding organizations of PHILFEJA
- Philippine Association of Japan Airline Scholars (PHILAJALS) – an association of Filipino participants in the annual Japan Airlines Summer Program which was discontinued in the late ‘90s
- Philippines-Japan Youth Club (PJYC) – an association of Filipino participants in the JASCAA Youth Program, which was discontinued in the early 2000s
- Philippines Japan Fellows Association (PHILJAFA) – an association of scholars and grantees of fellowships and trainings under various JICA programs, which in 2013 merged with similar groups of former JICA scholars into the JICA Alumni Association (JAAP); JAAP was officially accepted as a PHILFEJA Charter Association in October 2014 replacing PHILJAFA whose 50-year corporate life had expired.